[gmx-users] Re:Using virtual site

Dear Mark, You mean do the CO simulation and then add V-site upon production run? Could you please more specific, what has to be done to avoid this error? On Fri, Apr 26, 2013 at 6:16 PM, �� wrote: Maybe your starting configuration of atoms is too broken to

[gmx-users] doubt in mdrun

Sir, I studying the dynamics of a peptide in explicit solvent model.But during the mdrun I got the message like this. NOTE 1 [file md.mdp]: This run will generate roughly 1177130 Mb of data why the run generating this much amount of data? The md.mdp file I used is shown below title

[gmx-users] Re: gmx-users Digest, Vol 108, Issue 183

> > > This could be an underlying problem related to the above interpretation of > periodicity. We don't have enough information to say for sure yet. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Depa

[gmx-users] Re: gmx-users Digest, Vol 109, Issue 2

Sir My query is how to generate input file for umbrella sampling??? On Wed, May 1, 2013 at 6:34 AM, wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (gmx-users-requ...@gromacs.org) Add cleanup > rule

RE: [gmx-users] help with g_hydorder and g_polystat

Hello Justin, My mdp file shows that the pbc was set to xyz. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS

RE: [gmx-users] help with g_hydorder and g_polystat

Hello Justin, My mdp file shows that the pbc was set to xyz. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMAC

Re: [gmx-users] stable branch using git

On 4/30/13 8:50 PM, Sikandar Mashayak wrote: Hi Justin Thanks for explanation. But I am a bit confused because I am new to git. When I check out release-4-6 branch, the source code should be the same as the one in tarball from Gromacs website, right? When I run git status I get # On branch rel

Re: [gmx-users] stable branch using git

Hi Justin Thanks for explanation. But I am a bit confused because I am new to git. When I check out release-4-6 branch, the source code should be the same as the one in tarball from Gromacs website, right? When I run git status I get # On branch release-4-6 nothing to commit (working directory cle

Re: [gmx-users] stable branch using git

On 4/30/13 8:28 PM, Sikandar Mashayak wrote: Thanks Justin. I replaced release-4-5-patches with release-4-6 while checking out the branch. When I installed it and checked the version string I get VERSION 4.6.2-dev-20130429-d13fc48. Does that mean I got the version which is still under developm

Re: [gmx-users] local pressure

On 4/30/13 8:01 PM, Sikandar Mashayak wrote: Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0. I am wondering whether this code can compute the spatial variation of pressure in given system. And

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my sys

Re: [gmx-users] stable branch using git

Thanks Justin. I replaced release-4-5-patches with release-4-6 while checking out the branch. When I installed it and checked the version string I get VERSION 4.6.2-dev-20130429-d13fc48. Does that mean I got the version which is still under development and not stable and tested? Should I be concer

[gmx-users] local pressure

Hi I found the branch of gromacs code called localpressure-4.0 at http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0. I am wondering whether this code can compute the spatial variation of pressure in given system. And if it does, how stable is this branch? Are there

[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the sing

[gmx-users] Re: Fatal error: Failed to lock: md.log. Function not implemented.

hi, Justin, Thank you very much! Thank you! Ya, it's works! great! cool! Thank you very much for your suggestion, this time I also not use -reprod ,it doesn't effect simulation. Work also can go on! Thank you very much for your kind help! maggin -- View this message in context: http://gro

Re: [gmx-users] stable branch using git

On 4/30/13 3:03 PM, Sikandar Mashayak wrote: Hi I am following the git tutorial for the novice. It says to check out stable version one should use "git checkout --track -b release-4-5-patches origin/release-4-5-patches" Is there stable branch for 4.6? If yes, how do get it? I tried replacing

Re: [gmx-users] Umbrella sampling's equilibration runs

On 4/30/13 1:38 PM, James Starlight wrote: Justin, could you also tell me 1) what difference should be expected from the umbrella sampling run with (as I want to do for better coverage) and without (as in your tutorial) velocities re-assignment on each umbrella window run ? You have to dis

Re: Aw: [gmx-users] Re: how is the pulling force measured

On 4/30/13 12:33 PM, lloyd riggs wrote: I appologise, I meant defined at the same time without complaining, not just either direction. A different atom order is interpreted as a different interaction. In this case, if both are defined, there is indeed a difference in the improper energy ter

[gmx-users] stable branch using git

Hi I am following the git tutorial for the novice. It says to check out stable version one should use "git checkout --track -b release-4-5-patches origin/release-4-5-patches" Is there stable branch for 4.6? If yes, how do get it? I tried replacing 4-5 by 4-6 but I get the error: fatal: git checko

Re: [gmx-users] Umbrella sampling's equilibration runs

Justin, could you also tell me 1) what difference should be expected from the umbrella sampling run with (as I want to do for better coverage) and without (as in your tutorial) velocities re-assignment on each umbrella window run ? 2) On what suggestions should I chose each conformer from pullin

Aw: [gmx-users] Re: how is the pulling force measured

I appologise, I meant defined at the same time without complaining, not just either direction.   Gesendet: Montag, 29. April 2013 um 22:23 Uhr Von: "lloyd riggs" An: "S. Watkins" Betreff: Aw: [gmx-users] Re: how is the pulling force measured     Dear All, Doing a water/temp energy minimizati

Re: [gmx-users] help with g_hydorder and g_polystat

On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n

Re: [gmx-users] Umbrella sampling's equilibration runs

On 4/30/13 10:58 AM, James Starlight wrote: Dear Gromacs users! I have a question about umbrella sampling simulation based on the Justin's tutorial. According to the tutorial after definition of the set of conformers extracted from the pulled trajectory I should run N equilibrating simulatio

[gmx-users] Umbrella sampling's equilibration runs

Dear Gromacs users! I have a question about umbrella sampling simulation based on the Justin's tutorial. According to the tutorial after definition of the set of conformers extracted from the pulled trajectory I should run N equilibrating simulations and N productions runs. In the tutorial I've

[gmx-users] help with g_hydorder and g_polystat

Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Interna

Re: [gmx-users] Error in pdb2gmx

On 4/30/13 6:10 AM, Nikunj Maheshwari wrote: Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message ("Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ") when I used OPL

Re: [gmx-users] Error in pdb2gmx

Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message ("Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ") when I used OPLS, this time it was His 65. So I used -his optio

Re: [gmx-users] no such moleculetype

If you are starting a new topic, please give it an informative subject line and do not reply to a digest message. On 4/30/13 3:37 AM, Arunima Shilpi wrote: hello sir there was error in running grompp file of umbrella sampling... the error it says "no such molecule type sol" found... ho

Re: [gmx-users] Error in pdb2gmx

On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field "Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, th

Re: [gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.

On 4/29/13 9:30 PM, maggin wrote: Hi, when I use GROMACS4.5.5 to do peptid simulation. At NVT step, system is not equilibration, so I extend NVT simulation as follows: tpbconv -s nvt.tpr -extend 2000 -o next1.tpr mpirun -np 4 mdrun_mpi -reprod -s next1.tpr -cpi nvt.cpt after finish this e

[gmx-users] Re: how is the pulling force measured

I never looked into the code, but i understanded it the following way (for pull_geometry = distane, direction, position). For the pulling the reference group is held fixed and the force is applied to the pulled group. Since the reference group an move during the rest of the simulation (all steps

Re: [gmx-users] Re: genbox box size problem

We have noticed that g_genbox issue with MARTINI but have not new able to understand where it actually comes from. It might be a bug or just a miss communication of the vdw radius with genbox that appears only with large spheres. On Apr 29, 2013, at 19:50, "alex.bjorling" wrote: > Justin Le

[gmx-users] Re: how is the pulling force measured

2013/4/30 kim2811 [via GROMACS] > > Hi Alex, > > I read the manual but I got confused with the details. My pull_geometry = > position with pulling direction along y. I am trying to dissociate two > interacting proteins. So I set the last amino acid of one protein as my > reference group and the l

[gmx-users] Re: gmx-users Digest, Vol 108, Issue 140

hello sir there was error in running grompp file of umbrella sampling... the error it says "no such molecule type sol" found... how to debug the error On Tue, Apr 23, 2013 at 3:30 PM, wrote: > [image: Boxbe] This message is eligible > for Automatic Cle