Re: [gmx-users] (no subject)

Sorry I found this thread here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html >From my understanding, I use pdb2gmx on my entire output file, however, where does the data in the .psf file go? *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assis

[gmx-users] (no subject)

Hi all, I am trying to run grompp on POPC lipid bilayer that I constructed in CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI, however, I received the error: "No Default U-B Types" >From a few previous threads, it was suggested that I stripped the waters and use pdb2gm

[gmx-users] Setting Up "Equivalent" Runs With -notunepme

Hi everyone, From my understanding of the release notes for the gromacs-2016 versions, pretty much all of the settings that are tuned by tunepme can now be modified manually (modifying some of these settings still caused errors all the way up to gromacs-5.1.7). I'm not trying to make runs th

Re: [gmx-users] Restarting a simulation when checkpoint files are corrupted

Excellent! Thanks Mark! Yeah, already had a discussion with the sysadmin of this particular system; it was definitely not something that should happen. Cheers! David On 03/17/2017 10:11 AM, Mark Abraham wrote: > Hi, > > > On Fri, Mar 17, 2017 at 6:00 PM David Dotson wrote: > >> Greetings, >>

Re: [gmx-users] Restarting a simulation when checkpoint files are corrupted

Hi, On Fri, Mar 17, 2017 at 6:00 PM David Dotson wrote: > Greetings, > > I have a simulation that has been running for a long time, with many > trajectory segments (counting up to about 190). One of the segments ran on > a cluster that experienced a filesystem outage such that some of the files

[gmx-users] Restarting a simulation when checkpoint files are corrupted

Greetings, I have a simulation that has been running for a long time, with many trajectory segments (counting up to about 190). One of the segments ran on a cluster that experienced a filesystem outage such that some of the files for that run were corrupted, including its checkpoint files (both

[gmx-users] protein-ligand complex mdrun errors

respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

Re: [gmx-users] MDRUN doesn't print Hessian Matrix as ordered

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote: Thank you Justin for your replay. I've read that to compute specific heats (Cv or Cp) it is necessary calculating quantum correction (using the tool g_nmeig). Then, this tool calculates such a correction using the Hessian matrix. Is for that r

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

Thank you Justin for your replay. I've read that to compute specific heats (Cv or Cp) it is necessary calculating quantum correction (using the tool g_nmeig). Then, this tool calculates such a correction using the Hessian matrix. Is for that reason my interest in getting it. So, my question is why

Re: [gmx-users] MDRUN doesn't print Hessian Matrix as ordered.

On 3/17/17 8:20 AM, Juan José Galano Frutos wrote: Hi there: I am trying to calculate the specific heat (Cp) of my protein, but I should take into account quantum correction as indicated lately. Then, I need to obtain from the production step the Hessian Matrix including the eigenvectors neede

Re: [gmx-users] Doubt from force constant calculations

On 3/17/17 7:53 AM, Rakesh Pant wrote: Dear all, How to calculate force constant for bonds and angles using quantum chemistry calculations. Typically a vibrational analysis is done and force constants are set to reproduce the frequencies. -Justin -- =

Re: [gmx-users] Running GROMACS on cluster

On 3/17/17 7:22 AM, Yasser Almeida Hernández wrote: Hi all, I am strugling to run GROMACS on a cluster with SGE queue system, but I have any acceleration. The verbose output says that it will end is September 2017!!. This is the script I am using to run. What does your system administrator

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

On 3/17/17 1:40 AM, Devashish_Das wrote: Hello All, Presently we are working in generating dihedral drivers for AIB dipeptide in gromacs. We would like to create energy contour maps for different phi, psi angle for AIB in gromacs. We are unable to create the correct energy map vs phi/psi angle

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered.

Hi there: I am trying to calculate the specific heat (Cp) of my protein, but I should take into account quantum correction as indicated lately. Then, I need to obtain from the production step the Hessian Matrix including the eigenvectors needed to calculate the vibrational energy. So, the point is

[gmx-users] Doubt from force constant calculations

Dear all, How to calculate force constant for bonds and angles using quantum chemistry calculations. Thanks Rakesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.or

[gmx-users] Running GROMACS on cluster

Hi all, I am strugling to run GROMACS on a cluster with SGE queue system, but I have any acceleration. The verbose output says that it will end is September 2017!!. This is the script I am using to run. #!/bin/bash #$ -cwd #$ -pe parallel 24 #$ -q main.q #name of the queue #$ -e stderr.