[gmx-users] General questions about topology building

So the following question, if I want to change a few residues in a system that is already made (equilibrated, a protein in a lipid membrane), how should i go about that? What would be the protocol? I did it this way -> i first made a pdb out of the last frame (changed the 3 residues in Chimera)

[gmx-users] Getting charges of the system out of the simulation in human-readable form

So my question is, what is the most simple way to get a file with residue and atom types in addition to charges out of the files created at the end of the simulation? I tried dumping the .tpr file but its file structure is a bit too complicated, I'd preffer something easier. Also since I created

[gmx-users] Question regarding error

Why would such a command: gmx pdb2gmx -f system.pdb -i /home/bla/charmm36chol_psm_dopc.ff/PSM.itp -o systemprocessed.gro -water tip3p -ignh -ff charmm36chol_psm_dopc give me the following error: Fatal error: Residue 'PSM' not found in residue topology database For more information and tips fo

[gmx-users] How to remove ions from, and from which file in the finished simulation?

Hello, got another question, while I'm finding my way around Gromacs :). I have a simulation which I have to continue but I need to remove the ions out of it and add just so much ions back that the system will be neutral, because now there are too much of them. So I should be working on the .gr

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Thank you both for the answers, guess I have too low of a frame count on the earlier simulation by a colleague, gonna set up the simulation again with more frames being logged. :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-User

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Thanks. Still I was told that even if i set the "output frequency of frames" the .trr should contain more finer grained data? What file can I show you, that you can see more out from it? Regards, Marko -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

Micholas, I think it should be 2fs the timestep if you are reffering to that? I have the .trr file its 95gb, I should be able to make a xtc with 1ps step right? Marko -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] How to decrease the time gap between frames of an already made simulation

Hello, could you please advise regarding the correct command for decreaseing the time gap between frames of an already made simulation, from 20ps to 1ps. I tried these commands but they didn't work: gmx trjconv -s md.tpr -f md.trr -o md1pico.xtc -tu ps -skip 500 gmx trjconv -f md.trr -o md1p