RE: [gmx-users] Energy Conservation with 4fs timestep

> Date: Wed, 1 Apr 2009 14:15:05 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Energy Conservation with 4fs timestep > > Joe Joe wrote: > > Hi, > > > > I get good conservation when running NVE in gromacs with 4 fs when I use > > PME-switch for el

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

I wanted the OPLS-UA because my system is large (3 proteins with 2 organic molecules, in water), and, if the G43a1 forcefield gives me a MD speed of 70 ps/day, an all atom model will result much slower. So what else can I do to speed up my MD, to get results in 1-3 months?. Mensaje citado por David

RE: [gmx-users] How to calculate the dihedral angle variations ???

Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) dihedral angle during

Re: [gmx-users] How to calculate the dihedral angle variations ???

First of all Thanks for ur reply ! I tried both g_angle and g_chi with all suitable options, but i didn't get the required result.Can u plz help me in this regard ??? 2009/4/1 Antonia V. > > Did you try g_angle?? > > Antonia > -- > Date: Wed, 1 Apr 2009 11:35:29 +0530

[gmx-users] (no subject)

Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at addre

Re: [gmx-users] How to calculate the dihedral angle variations ???

Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what

Re: [gmx-users] How to calculate the dihedral angle variations ???

Hai Sir ! Actually i want to see the dihedral angle (Cβ-S-S-Cβ) variation over time.I used the commands "g_angle -f trajout.xtc -s gp123_b4full.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oc dihcorr.xvg -type dihedral -all" "g_chi -s gp123_full.gro -f gp123

Re: [gmx-users] (no subject)

Antonia V. wrote: Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01

[gmx-users] Gromacs 4.0.2 vs. 4.0.3

Hi, we performed for comparison pentadecane simulations using both the 4.0.2 version and 4.0.3, with the same mdp file (see below). Results look quite different (reproducible), for 4.0.2 the system quickly (few 100 ps) enters the crystalline phase while it stays fluid for 4.0.3 (with an i

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought you have missed my comments (see below). Now we h

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't only a thank-email). Since it took so long, and other similar discussions are still running I thought

RE: [gmx-users] Gromacs 4.0.2 vs. 4.0.3

Hi, The release notes for 4.0.3 are at: http://www.gromacs.org/content/view/181/132/ I don't see any relevant bug fixes there and I don't recall any either. Please update to 4.0.4, since many small bugs have been fixed. Berk > From: rai...@bioinformatik.uni-saarland.de > To: gmx-users@gromacs.

[gmx-users] GROMOS carbohydrate forcefield 45a4

Dear List, In the paper entitled "A new GROMOS force field for hexopyranose-based carbohydrates" Journal of Computational Chemistry Volume 26 Issue 13, Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once the conformation is stabilised in chair, they donot observe any further tran

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system! Is it maybe the prote

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Edvin Erdtman wrote: Hi We have tried with no cutoff, as I have written in former emails, but that was when we got trouble with LINCS warnings. We then thought that we could try to continue remove lipids in the compression-steps to get rid of that LINCS warnings, and to have a stable system

[gmx-users] Error with equilibration of DPPC membrane with protein

Try gromacs 3.1.4 make_hole version, downloadable from the user contributions page. This works well for me. Alternatively, just select a bunch of lipids to remove based on g_mindist and equilibrate -- 50ns is cheap nowadays. The only reason that inflategro might be a huge advantage is if yo

[gmx-users] Problems with Jacobi diagonalization

Greetings--- I'm working with a DNA system, and all of the routines I've worked with that require Jacobi diagonalization (g_covar, g_rms, etc) fail with the "Too many iterations in routine JACOBI" error. I'm using gromacs-3.3.3 with ffamber99 on the NCSA Mercury cluster. I've searched the archives,

RE: [gmx-users] (no subject)

> 1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. > 2. Anything else that was printed to screen or the .log file (that's where > the > real error message will appear) On the screen the message was [compute-0-4:01361] ***

Re: [gmx-users] (no subject)

Antonia V. wrote: > 1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. > 2. Anything else that was printed to screen or the .log file (that's where the > real error message will appear) On the screen the message was [c

RE: [gmx-users] (no subject)

I switched to v-rescale for the thermostat and things look normal! Thanks for the help Antonia > Date: Wed, 1 Apr 2009 12:11:47 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) > > > > Antonia V. wrote: > > > 1. A description of your system >

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to con

Re: [gmx-users] Energy Conservation with 4fs timestep

rlist 1.3 did the trick, thanks. Why did I not see this problem with PME-switch? Thanks, Ilya 2009/4/1 Berk Hess > > > > Date: Wed, 1 Apr 2009 14:15:05 +1100 > > From: mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Energy Conservation with 4fs timestep > >

Re: [gmx-users] GROMOS carbohydrate forcefield 45a4

Neha Gandhi wrote: Dear List, In the paper entitled "A new GROMOS force field for hexopyranose-based carbohydrates" Journal of Computational Chemistry Volume 26 Issue 13, Pages 1400 - 1412. When the authors ran unrestrained md for 2ns, once the conformation is stabilised in chair, they donot o

[gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds

Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus, the atoms are indeed located

Re: [gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds

darre...@ece.ubc.ca wrote: Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus,

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Tsjerk, Thank you for your quick and helpful response. I defined "xtc_grps = TDR" in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't understand what "shuffling" o

Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Hi Tsjerk, Thank you for your quick and helpful response. I defined "xtc_grps = TDR" in my .mdp file (then I use grompp -f mdpme.mdp -c confout.gro -p topol.top -o topol.tpr -np 8 -n index.ndx, index contains TDR and SOL) and run it with -np 8. I'm afraid that I don't un

RE: [gmx-users] How to calculate the dihedral angle variations ???

g_angle will do that fine, and with the options you used it should have done so. Possible issue that may make that fail is you failed to generate the correct angle index file for the dihedral(s) of interest. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Ph

Re: [gmx-users] problem in energy minimization

Hi Mark Sorry for the delayed reply. Somehow I missed your mail that time. I am doing exactly what you have suggested. I am building up this missing part and then trying to run the simulation. Again 'm sorry for this delay. Best regards, Abhik Abhik Mukhopadhyay Departamento Química / Faculd

Re: [gmx-users] Problems with Jacobi diagonalization

Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12284, but I still can't ge

Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that t

Re: [gmx-users] Problems with Jacobi diagonalization

Justin A. Lemkul wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is Indeed, that's the problem, then! the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and

Re: [gmx-users] Problems with Jacobi diagonalization

Or rather than modifying the .top use tpbconv with an index file to generate a new .tpr Tom --On Wednesday, April 01, 2009 21:15:34 -0400 "Justin A. Lemkul" wrote: Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.x

Re: [gmx-users] Problems with Jacobi diagonalization

Thanks, Mark- I re-ran a short MD simulation with TDR as the only xtc group, and used tpbconv to create a .tpr file with only TDR (tpxout.tpr) and ran g_covar with an index.ndx that contains only TPR (just to be safe!), g_covar -f traj.xtc -s tpxout.tpr -ref -n index.ndx and I still get the Jacob

[gmx-users] compilation error

Hello, I need some help figuring out how to compile gromacs on and sgi or linux machine. This is the error I get after using the make command to compile gromacs. Need some suggestions. Thanks source='gmx_wham.c' object='gmx_wham.lo' libtool=yes \     DEPDIR=.deps depmode=sgi /bin/sh

Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

>Date: Wed, 01 Apr 2009 22:38:28 +0200 >From: David van der Spoel >Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum) > not recognizing bonds >To: Discussion list for GROMACS users >Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se> >Content-Type: text/plain; charset=ISO-8

Re: [gmx-users] compilation error

yimnai forlemu wrote: Hello, I need some help figuring out how to compile gromacs on and sgi or linux machine. This is the error I get after using the make command to compile gromacs. Need some suggestions. Thanks What compiler and compiler version are you using? It looks archaic, from th