Re: [gmx-users] make_ndx unable to save

ram bio wrote: Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containi

Re: [gmx-users] Negative Pressure After Energy Minimization

Saumya wrote: Hello all, I am simulating a DMPC Lipid Bilayer and after running the energy minimization, I obtained negative values for the pressure. Is it normal to have those values? If not, How can I fix that? Kindly guide. Instantaneous pressure values are rather meaningless, especia

[gmx-users] make_ndx unable to save

Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups, but

[gmx-users] Negative Pressure After Energy Minimization

Hello all, I am simulating a DMPC Lipid Bilayer and after running the energy minimization, I obtained negative values for the pressure. Is it normal to have those values? If not, How can I fix that? Kindly guide. Regards, Saumya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] REMD problem

Liu, Liang wrote: Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( What structure(s)? The .xtc files contain the coordina