Re: [gmx-users] How I extend command

Hi Abid, To extend a run I use something like this For 50 ns tpbconv -s previous.tpr -extend 5 -o next.tpr mdrun -s next.tpr -cpi previous.cpt Rohit On Tue, Feb 24, 2015 at 4:03 AM, Abid Channa wrote: > Hi gromacs users, > > I am working membrane complex simulation of 20 > ns, 100, s

Re: [gmx-users] Error during mdrun

Hi Soumadwip, I my understanding this error occurs when GROMACS can't distribute your job on the number of cores you are asking. Try to change the number of cores from 80 to something else, probably a fewer number of cores. I had this error once and I figured out that was the reason, but I am not

Re: [gmx-users] fe2s2 simulation

Hi Somlata, For GROMACS to recognize your FES moiety you will have to determine the force field parameters for the forcefield which you want to use and then update the GROMACS databases. Without GOMACS having the necessary parameters for the atoms in your FES moiety in its forcefield database you

[gmx-users] fitting problem

Hi there, I am trying to fit a protein to a reference structure using the command below trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive I am using protein for least square and system for output. This command always worked for me but for this particular protein the side chains get

[gmx-users] trj_cavity segmentation fault

Hi there, I am trying to us trj_cavity to detect cavity formation and volume in my simulation. The plugin installed with no problem but no matter how I run it, it always gives segmentation fault. Can anyone please help me out with this. Alternatively if anyone knows an alternative software to det

Re: [gmx-users] Centring a protein complex

an artefact and not that its actually broken. But is there a way to make then look whole. I tried the option whole with -pbc but couldn't figure out what it actually did. Thanks Rohit On Wed, Oct 29, 2014 at 12:22 PM, Justin Lemkul wrote: > > > On 10/29/14 8:08 AM, Rohit Farmer

[gmx-users] Centring a protein complex

Hi Guys, I am trying to centre a protein complex using this command trjconv -pbc mol -center -ur compact -s em.tpr -f md_0.xtc -o md_0_center.xtc I selected "protein" in the first option and then "system" in the second for output but I received the following error Floating point exception1900.0

Re: [gmx-users] Parameter conversion from GAFF to Gromacs

Thanks Justin On Thu, Oct 16, 2014 at 6:29 PM, Justin Lemkul wrote: > > > On 10/16/14 1:24 PM, Rohit Farmer wrote: > >> Hi All, >> >> I have recently converted the whole of GAFF parameters database to Gromacs >> format to use with the AMBER 99SB ILDN forcefi

[gmx-users] Parameter conversion from GAFF to Gromacs

Hi All, I have recently converted the whole of GAFF parameters database to Gromacs format to use with the AMBER 99SB ILDN forcefield. My intention was to simulate a number of ligands which I covalently bound to a residue in the protein. So if I bind something to a residue then I am effectively add