From: Gianluca Interlandi (gianluca_at_u. On Wed, Sep 23, 2015 at 02:28:07PM -0700, Gianluca Interlandi wrote: > The other question in the decision SSD vs HDD is the price tag. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. To: Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Specifically, I’m testing different binding domains. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ]. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. From: Gianluca Interlandi (gianluca_at_u. Be the first to write a review. washington. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. From: Gianluca Interlandi (gianluca_at_u. Stenkamp, 3 Wendy E. washington. 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. washington. washington. 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. 1002/prot. From: Gianluca Interlandi (gianluca_at_u. uiuc. From: John Stone (johns_at_ks. 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 Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. 7 released. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. The server where VMD is started from has On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. Skip to search form Skip to main content Skip to account menu. uiuc. washington. I needed to install the 'patch' program. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. From: Mitchell Gleed (aliigleed16_at_gmail. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. washington. washington. Re: replica exchange and GPU acceleration. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. Re: Help building a desktop for namd. I was recording the energies once every 100 steps. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. It's > slightly faster but still not that much faster than running on 16 CPU cores. I would like to erase Windows and install Leap 42. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. Languages: English, Spanish, Italian. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. I made those videos seven years ago. washington. VMD-L Mailing List. 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. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. washington. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. 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. Bidet · Toilet · Shower. 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: 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. Balcony. 7b1 on NCSA Abe. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. I > would be happy if somebody could point me out to some scripts which help me > perform 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). 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. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. washington. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. 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: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Sat Jul 04 2015 - 15:33:25 CDT Next message: VINAYAK BHAT: "Generating solvent models. Semantic Scholar's Logo. 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. Sokurenko 1 , *. . Forest, Academic Editor. 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. washington. 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. > > I have already run a bunch of pulling simulations in the NVE ensemble. edu> wrote: > Roy, > > I think that you are confusing two things. 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> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. }, author={Dagmara I. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. I made those videos seven years ago. Kitchen. The only significant change since 2. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Electrical Engineering. Jennifer KongRE: DCD. RE: Force field design. 1 on it using Legacy Bios and a. New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. Next in thread: Gianluca Interlandi: "Re: NAMD 2. washington. 7 with the PLUMED patch. washington. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiReply: 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. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. Author Profile. 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. PMID: 37700555; DOI: 10. Gianluca has 2 jobs listed on their profile. From: Gianluca Interlandi (gianluca_at_u. uiuc. In reply to: Gianluca Interlandi: "Compiling NAMD 2. Email:. View the profiles of people named Gianluca Interlandi. From: Gianluca Interlandi (gianluca_at_u. I needed to install the 'patch' program. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. . 50% refund of amount payable if you cancel at least 7 days before check-in. edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). Justin Kollman Professor. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). You should simulateCorresponding Author. Join Facebook to connect with Gianluca Interlandi and others you may know. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. I know this can be just a detail, but it is quite tricky. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. From: Gianluca Interlandi (gianluca_at_u. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). I also ran a non-CUDA job on Forge > using 16 CPUs. 10. PMID: 37700555; DOI: 10. But, using the PBC my protein is continuous. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. washington. washington. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. washington. J. uiuc. edu> wrote: > I'm cc'ing here the NAMD list so that others. , and Thomas W. uiuc. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. 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). However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. Previous message: Gianluca Interlandi: "NAMD 2. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. It's > slightly faster but still not that much faster than running on 16 CPU cores. 6 ns/day for a 100k atom system with roughly those same parameters (and. Just source the Tcl file and use the 'unwrap' procedure. edu> > wrote:Re: Help building a desktop for namd. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. From: Gianluca Interlandi (gianluca_at_u. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. edu) Date: Wed Sep 23 2015 - 13:37:27 CDT Next message: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Previous message: Mayne, Christopher G: "Re: FFTK Bond optimization" In reply to: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Next in thread: Gianluca Interlandi: "Re:. washington. From: Gianluca Interlandi (gianluca_at_u. I’m working in Research Assistant Professor Gianluca Interlandi’s research lab, and I study the behavior of the Von Willebrand factor (VWF), which is a plasma protein that recruits platelets to the site of blood vessel injury. washington. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. washington. From: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Search for: Main Menu. washington. 7b4 is thatRE: DCD. 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. edu> > wrote:From: Gianluca Interlandi [gianluca_at_u. Katrina T. washington. I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: 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:. 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. From: Gianluca Interlandi [gianluca_at_u. washington. 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. washington. washington. 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. From: Gianluca Interlandi (gianluca_at_u. Bedrooms: 1 (People: 2) Bedroom 1. 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)"Re: namd ibverbs. 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. washington. washington. edu> > wrote: > Roy, > > I think that you are confusing two things. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallRe: Help building a desktop for namd. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. 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. washington. PMID: 33550613 PMCID: PMC8089038 DOI: 10. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. Gianluca Interlandi Research Assistant Professor. 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. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. 7 out the door on Friday. Michel Espinoza-Fonseca: "Re: Vibrational. washington. edu) Date: Wed Oct 20 2010 - 15:33:33 CDT Next message: jnsong: "how to cenvert NAMD binary coordinate file to text file" Previous message: Jim Phillips: "Re: NAMD 2. washington. uiuc. 1002/prot. AMBER does, and so does GROMACS. 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. Gianluca Interlandi, Department of Bioengineering, University of Washington, Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. washington. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. From: Axel Kohlmeyer (akohlmey_at_gmail. There have been over 180 downloads and no complaints so far. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. One of the. From: Gianluca Interlandi (gianluca_at_u. uiuc. 5923 Kcal/mol also we have 6. I thought that free Dagmara I. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. 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. washington. Search 214,979,228 papers from all fields of science. Whitfield, 2 Esther Bullitt, 4 Ronald E. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. ch +41 (0) 1 635 55 93SMD on center of mass. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. edu> Cc: <namd-l_at_ks. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. 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. MyFrom: Gianluca Interlandi (gianluca_at_u. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. That file contains information how to run >> NAMD (and also compile it. 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"> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. washington. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. washington. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. edu> wrote: > Roy, > > I think that you are confusing two things. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. Academic ProgramsFrom: Gianluca Interlandi (gianluca_at_u. 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. Citat Gianluca Interlandi <gianluca_at_bioc. The simulations were not performed at constant velocity > but at constant force. Abstract. edu. washington. 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. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. washington. washington. 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:. washington. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. 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. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. From: Gianluca Interlandi (gianluca_at_u. washington. Gianluca Interlandi. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. edu> wrote:From: Gianluca Interlandi (gianluca_at_u. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> 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 small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performDCD. 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. 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)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. It's > slightly faster but still not that much faster than running on 16 CPU cores. g. Next in thread: Gianluca Interlandi: "Re: namd-l: DCD for windows" Messages sorted by: [ attachment ] Hi, We don't have a build of catdcd for windows currently, but it should be possible to make one. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. From: Gianluca Interlandi (gianluca_at_u. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? Next in thread: Gianluca Interlandi: "Re: NAMD 2. 7 ns/day, which seems decent given the system size. Neil King Assistant Professor. > > 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):. 6 ns/day for a 100k atom system with roughly those same parameters (and. July; 84 (7):990–1008. From: Gianluca Interlandi (gianluca_at_u. Re: Abe versus Lincoln. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. In the text > field you can enter your atom selection, e. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. 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. From: Gianluca Interlandi (gianluca_at_u. m. edu> wrote: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. g. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. 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. 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. Re: Help building a desktop for namd. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. washington. Rachel Klevit WRF Endowed Chair in Biochemistry. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you canThe bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. edu) Date: Thu Apr 30 2009 - 12:15:37 CDT Next message: bo liu: "Re: Optimizing configuration option for fast calculations" Previous message: Jerome Henin: "Re: Benzene PSF" In reply to: Peter Freddolino: "Re: NAMD 2. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message:. washington. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. Policies. From: Gianluca Interlandi (gianluca_at_u. 7 ns/day, which seems decent given the system size. Hope the video helps, but now I'm embarrassed. washington. g. Next in thread: Gianluca Interlandi: "Re: NAMD 2. >From: Gianluca Interlandi (gianluca_at_u. 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. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling.