Re: [gmx-users] Electrostatic potential

I can't figure out how to put the coulombic potential only between residues in chain A and residues in chain B, but not between residues that are in the same chain. Thanks, Esteban 2010/8/28 Justin A. Lemkul > > > ithu wrote: > >> Hi everybody, >> >> I

[gmx-users] Electrostatic potential

Hi everybody, I want to apply a coulombic potential between charged residues in a coarse-grain model, but between residues that belong to different chains of a protein complex. Both chains are name as molecule A and molecule B in the topology file. Thank you very much, Esteban -- gmx-users maili

[gmx-users] protein broken

Hi All! I do my md simulation but the protein moves out of the box, so it seems that the protein is broken in .trr and .xtc file. I try to use trjconv to put the protein back into the box and make the protein whole. The command is like below: trjconv -f 18pTTAD-Taz2-water.gro -s 18pTTAD-Taz2-water

[gmx-users] Implicit solvent

Dear gromacs Users, I found this in the web, but I wanted to know if there exists the possibility now of using implicit solvent efficiently. Thanks, Esteban A repeating question on the mailing list whether GROMACS can perform implicit solvent simulations. The answer is, not really. Over the last

[gmx-users] Topologies phosphoserine and phosphothreonine for ffamber99

Hi. I am trying tu run a protein under the ffamber99 force field. Has anyone used a topology of phosphoserine and phosphothreonine for this force field? Thanks, Esteban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive