Re: [gmx-users] Force field transformation from Gromacs to Charmm format

On 12/18/16 12:22 PM, Dawid das wrote: Dear All, Have you ever seen a script/tool that allows for transformation of the Gromacs force field files into CHARMM force field files? I can see that there is a Pythons script that does the other way around. Also I could use a tool that creates *.psf

Re: [gmx-users] Extending simulation, quick question

On 12/18/16 9:53 AM, Dario Akaberi wrote: Hello, I have a quick question. I've extended a simulation using the commnds: convert-tpr -s md_3.tpr -extend 1 -o md_3_next.tpr followed by mdrun -s md_3_next.tpr -cpi md_3_prev.cpt My questions are: 1) should I use the md_3_prev.cpt file

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Hi, All I know is that you've reported that nothing is obviously wrong :-) Mark On Sun, 18 Dec 2016 19:10 #SUKRITI GUPTA# wrote: > Hi Mark, > > > Thanks for the prompt reply. So continuing with the same shouldn't be an > issue right? > > Regards > > Sukriti > [ >

Re: [gmx-users] Charged systems

Can anyone please help me with this. Regards Sukriti

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 152, Issue 61

Hi Mark, Is the lowest drift in Figure 3.5, ~1e-6 kj/mol/atom/ps, as good as it gets? If the drift can be further reduced, how would one do this? Thanks, Mike On 12/17/2016 11:29 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list

[gmx-users] autocorrelation function

Dear Gromacs users, I calculate autocorrelation function of Rg using the following command: gmx analyze -f gyrate.xvg -o ac now I have two questions: 1) when I obtain Rg there are 3 columns in the file including Rg, Rg x, Rg y, and Rg z, respectively. Is this trend correct for the acf file,

[gmx-users] Force field transformation from Gromacs to Charmm format

Dear All, Have you ever seen a script/tool that allows for transformation of the Gromacs force field files into CHARMM force field files? I can see that there is a Pythons script that does the other way around. Also I could use a tool that creates *.psf file from *.top file. I googled for that

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Hi Mark, Thanks for the prompt reply. So continuing with the same shouldn't be an issue right? Regards Sukriti

[gmx-users] (no subject)

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Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Hi, Well that is fine. You were presumably running a minimisation to relax the structure to permit things to run. That a different path for minimisation didn't work is not necessarily of interest. Mark On Sun, 18 Dec 2016 19:01 #SUKRITI GUPTA# wrote: > Hi Mark, > > >

[gmx-users] Found solution to the problem of same rdfs for different residues

Dear Mark, Thanks a lot for drawing my attention repeatedly to the atom indices I was choosing for making the index file. I chose the atoms using the command 'a O r1' thinking it'll choose the oxygen atom of residue 1. Instead to my surprise,all the oxygen atoms of all residues were selected. I

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Hi Mark, When I complete energy minimization in version 4.5.5, I am able to run npt and nvt runs in new version i.e. 5.1.2. Regards Sukriti

[gmx-users] Extending simulation, quick question

Hello, I have a quick question. I've extended a simulation using the commnds: convert-tpr -s md_3.tpr -extend 1 -o md_3_next.tpr followed by mdrun -s md_3_next.tpr -cpi md_3_prev.cpt My questions are: 1) should I use the md_3_prev.cpt file or the md_3.cpt file? are these two file the

Re: [gmx-users] Force field transformation from Gromacs to Charmm format

Thank you! I will definitely have a close look at that. Best regards, Dawid 2016-12-19 2:33 GMT+01:00 Justin Lemkul : > > > On 12/18/16 12:22 PM, Dawid das wrote: > >> Dear All, >> >> Have you ever seen a script/tool that allows for transformation of the >> Gromacs force field