washington. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. washington. edu > <mailto:gianluca_at_u. Re: NAMD 2. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. washington. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. washington. I doubt that there is a way to have NAMD output theGianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>@article{Kisiela2015EffectOM, title={Effect of mAb926 and mAb475 on biofilm formed by E. washington. ch +41 (0) 1 635 55 93SMD on center of mass. Location info. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. m. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. washington. From: Stern, Julie (jvstern_at_bnl. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. But if you simulate entire proteins, charged termini. > However, topology and parameters for water and ions are. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. washington. uiuc. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. PMID: 37700555; DOI: 10. uiuc. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. Semantic Scholar's Logo. Re: external force. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Katrina T. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. >Re: Vibrational mode analysis. 7b1 on NCSA Abe. washington. Thanks for the reply. Living Room. washington. Gianluca From: Gianluca Interlandi (gianluca_at_u. Facebook gives people the power to share and makes the world more open and connected. edu) Date: Tue Aug 04 2009 - 00:36:38 CDT Next message: Nicholas M Glykos: "Re: A script for performing calculations divided by quanta" Previous message: Joshua Adelman: "Re: A script for performing calculations divided by quanta". Just a good MD toy ! Victor owner-namd-l_at_ks. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. From: Mitchell Gleed (aliigleed16_at_gmail. Research Assistant Professor [email protected]> > wrote:VMD-L Mailing List. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. That's why one wants to use a low value for the damping constant, in principle. What are you trying to accomplish? Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a js Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi! Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: > Roy, > > I think that you are confusing two things. Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. From: Gianluca Interlandi (gianluca_at_u. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. In the NAMD folder that you downloaded there >> is a file called "notes. Policies. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. The only significant change since 2. July; 84 (7):990–1008. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). (did you see if any hunk failed?)Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. 7 ns/day, which seems decent given the system size. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. washington. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. I'm > not sure whether the CHARMM program can read. I thought that free Dagmara I. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. NAMD supports CHARMM22 parameter files. Previous message: Gianluca Interlandi: "NAMD 2. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. washington. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. washington. . Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. Interlandi Mortgage Consultants, LLC Dec 2008 - Present 14 years 3 months. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. I also ran a non-CUDA job on Forge > using 16 CPUs. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. From: Gianluca Interlandi (gianluca_at_u. edu]Reply All Saturday,. Display options. Choose File -> Save Coordinates. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). At some point there will be a web page here. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. washington. washington. Interlandi G. Re: query about wrapped coordinates. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass""wrapAll on" with a complex. washington. washington. washington. , and Thomas W. From: Gianluca Interlandi (gianluca_at_u. 7b1 on NCSA. You should simulate it in explicit water (or try one of the implicitGianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. Search for: Main Menu. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. Re: Abe versus Lincoln. washington. Join Facebook to connect with Gianluca Interlandi and others you may know. The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. Anton. washington. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. October 10, 2019 - Present·Syracuse, Italy Da Host fai da te a Imprenditore Extra Alberghiero Owner and Founder at Baroque Apartments Syracuse, Italy Agenzia di affitti. From: Gianluca Interlandi (gianluca_at_u. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu> wrote:Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. washington. > From: Gianluca Interlandi [gianluca_at_u. washington. washington. washington. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. uiuc. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. }, author={Dagmara I. edu> wrote: > Roy, > > I think that you are confusing two things. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. > > > > Forget about creating a pdb file. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. I would be > happy if somebody could point me out to some scripts which help me performDCD. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. washington. From: Victor Kwan (vkwan8_at_uwo. edu Search for more papers by this author> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. 2020-10-26T08:31:24-07:00 September 9th, 2014 | Read More UW Bioengineering Summer Camp 2014 concludes, teaches high school students about bioengineering, global health. washington. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. washington. From: Gianluca Interlandi (gianluca_at_u. washington. by G. From: Ernesto Vargas (vargaslo_at_gmail. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Here they are: a. Forest, Academic Editor. But, using the PBC my protein is continuous. Eric Klavins Professor. washington. washington. washington. Gianluca Interlandi [email protected] orcid. 6 ns/day for a 100k atom system with roughly those same parameters (and. washington. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. washington. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. From: Gianluca Interlandi (gianluca_at_u. Bidet · Toilet · Shower. Languages spoken: English. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" From: Gianluca Interlandi (gianluca_at_u. Search 214,979,228 papers from all fields of science. In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. 7 with the PLUMED patch. Chemistry. , and Thomas W. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. Comparative controls consisted of FocH (high affinity with and. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. washington. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. . washington. Re: Protein in/out of box. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Entertainment. I was recording the energies once every 100 steps. I > > attach a plot of a constant velocity simulation where I'm pulling two > > proteins apart. Sarah Keller Professor. washington. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. 1 on it using Legacy Bios and a. washington. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. Gianluca Interlandi , Contributed equally to this work with: Pavel Aprikian, Gianluca Interlandi Affiliation Department of Bioengineering, University of Washington, Seattle, Washington, United. unizh. edu> > wrote:Re: Help building a desktop for namd. From: Gianluca Interlandi (gianluca_at_u. washington. The simulations were not performed at constant velocity > but at constant force. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. edu]Reply All Saturday,. From: Gianluca Interlandi (gianluca_at_u. washington. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. To: Gianluca Interlandi <gianluca_at_u. washington. 7 released" In reply to: Jim Phillips: "Re: NAMD 2. Re: Yet another NAMD speed concerns. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Wed Dec 12 2012 - 14:49:46 CST Next message: JC Gumbart: "Re: NAMD and new FF CHARMM36" Previous message: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" In reply to: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" Next in thread: Jeffrey Potoff: "Re: NAMD and new FF CHARMM36" > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. washington. I am > using the option "wrapAll on". The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. washington. washington. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Locking up the spike protein to prevent infection. Re: Vibrational mode analysis. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. Spaces. From: Victor (ovchinnv_at_gmx. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. washington. From: Gianluca Interlandi (gianluca_at_u. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce the. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. washington. I have to run following commands 2 times in tcl. From: Gianluca Interlandi (gianluca_at_u. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. Just a good MD toy ! Victor owner-namd-l_at_ks. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. washington. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. 15 K 1 KT = 2. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. at 298. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. It is experimentally knownReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. washington. From: Buddhadev Maiti (bmaiti_at_gsu. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. INVENTING THE FUTURE OF MEDICINE. There have been over 180 downloadsGianluca Interlandi, Wendy Thomas, The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations, "Proteins: Structure, Function, and Bioinformatics",. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. uiuc. washington. Gianluca Interlandi, Department of Bioengineering, University of Washington, Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. edu> wrote:Gianluca Interlandi. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. washington. upenn. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). > > I have already run a bunch of pulling simulations in the NVE ensemble. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. edu>: > Dear NAMD users, > > Is it possible to perform Poisson Boltzmann calculation with NAMD? > > I have simulated the wildtype and a single-point mutant of a protein. at 298. Friend and Aachal Jalan and Shivani Gupta and Gianluca Interlandi and Yan Liu* and Veronika Tchesnokova. uiuc. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi. RE: Force field design. washington. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Gianluca Interlandi composed on 2017-01-23 13:40 (UTC-0800):. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. washington. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. C; the more troublesome part is the lack of long-range electrostatic treatments. edu on behalf of Gianluca Interlandi [gianluca_at_u. From: bharat gupta (bharat. There have been over 180 downloadsReply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. 100% refund of amount payable if you cancel at least 14 days before check-in. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. A 1 TB > Samsung Evo 850 Pro costs 470$, a 1 TB Intel costs ~ 600$ and a PCIe Intel > 1 TB is over 2000$. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > I'm cc'ing here the NAMD list so that others. edu) Date: Tue Oct 31 2023 - 21:41:13 CDT Next message: Vasista: "STRIDE breaks after 100,000 protein atoms" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA". edu> wrote:From: Gianluca Interlandi (gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Choose File -> Save Coordinates. The read speed of the trajectory will go much faster if you select the "load all at once" checkbox in the moleculeRe: Vibrational mode analysis. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorGianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by. Gianluca has 2 jobs listed on their profile. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. What this rental offers. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass"Re: Abe versus Lincoln. 9. From: Gianluca Interlandi (gianluca_at_u. washington. washington. From: Gianluca Interlandi (gianluca_at_u. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the. I know this can be just a detail, but it is quite tricky. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. 50% refund of amount payable if you cancel at least 7 days before check-in. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. You should simulate it in explicit water (or try one of the implicitFrom: Gianluca Interlandi <gianluca_at_u. washington. washington. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. From: Gianluca Interlandi (gianluca_at_u. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington.