Re: [gmx-users] [gmx-developers] Gromacs Project Query

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

[gmx-users] Error while running grompp command

Hello, I am running the gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr And this is the error I am getting: ERROR 1 [file rew.prm, line 36]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block

Re: [gmx-users] syntax for index file in "gmx distance"

Hi http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions Em dom, 17 de fev de 2019 09:22, ZHANG Cheng <272699...@qq.com escreveu: > I think I know now: > > > gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 > plus

Re: [gmx-users] Probability of number of atomic contacts

Thank you very much, Justin! I tried this command: gmx_seq analyze -f numcont.xvg -dist num_dist.xvg and I got a histogram. Now the number of contacts between the ion and the polymer is between 160-180. I just want to be sure if I am doing this analysis correct. When I use gmx mindist, from

Re: [gmx-users] Probability of number of atomic contacts

On 2/17/19 7:21 AM, Mahsa wrote: Dear Gromacs users, I want to get histograms of the number of polymer-ion contacts average across the simulation. For this I used, gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od mindist.xvg -on numcont.xvg -or mindistres.xvg -group and from

Re: [gmx-users] syntax for index file in "gmx distance"

I think I know now: gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 plus group 1' -oall -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Sun, Feb 17, 2019 08:06 PM To: "gromacs.org_gmx-users"; Subject: syntax for

[gmx-users] Probability of number of atomic contacts

Dear Gromacs users, I want to get histograms of the number of polymer-ion contacts average across the simulation. For this I used, gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od mindist.xvg -on numcont.xvg -or mindistres.xvg -group and from the index file, I chose the ion first

[gmx-users] syntax for index file in "gmx distance"

My gro file looks like this $ Martini system from C226S.pdb $ 72758 $ 1ASP BB1 15.982 3.547 3.592 $ 1ASPSC12 15.989 3.335 3.842 $ 2ILE BB3 15.668 3.625 3.593 $ 2ILESC14 15.538 3.345 3.620 $ 3GLN BB5 15.590 3.886