[gmx-users] trjconv - more than one box

Dear Gromacs users, I was wondering if one can use trjconv to get a .pdb file which shows more than one box? Just like the "genconf -nbox" command but with trajectories? Thanks a lot Markus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] jointly-couple lipids to theromstat - MARTINI force-field

Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: << MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your

RE: [gmx-users] how to add potassium

Thank you very much. I managed meanwhile to run the simulation with K+ by adding <<>> to my ffnonbonded.itp I took c6 and c12 parameters (I use gromos 53a6) from Table I of Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers ' As

[gmx-users] how to add potassium

Dear all, I do not manage to add potassium ions to my system correctly. I foraged in the mailing list and tried to follow all advices, but it does not work out for me. It would be great if anybody could give me some advice. (here my so-far futile- procedure) 1

[gmx-users] use g_mindist to generate restraints

Dear gromacs users, I wonder if it would be possible to generate restraints in the following manner: I do simulations of a peptide embedded in a lipid bilayer and I have experimental NMR data which reflect the number of water molecules within a radius of ~ 0.9 - 1.0 nm for several carbons of m