[gmx-users] Pushing MD further

Hi, I am currently running some GPRC MD with membrane. After a lot of trial I now have a nice 25 ns run with an agonist. But the final structure is too close the starting and I know it is far from what the biology describes. I would like to know if there is options that I can add to my md.mdp fil

[gmx-users] RE: gmx-users Digest, Vol 66, Issue 124

Thielges, Sabine wrote: >> Hi everyone, >> >> I am currently doing a simulation which involves a dopamine receptor >> placed in a POPC membrane and an agonist or antagonist in the active >> site. The ligand was placed by VS and is closed to what the biology &g

[gmx-users] Ligand during GPRC-membrane simulation

Hi everyone, I am currently doing a simulation which involves a dopamine receptor placed in a POPC membrane and an agonist or antagonist in the active site. The ligand was placed by VS and is closed to what the biology gives. My problem is that the ligand get out of is normal position during the s

[gmx-users] problem with g_oder : file empty

.trr -n sn1_check.ndx -d z -od deuter_sn1_check.xvg # # g_order is part of G R O M A C S: # # Green Red Orange Magenta Azure Cyan Skyblue # @title "Deuterium order parameters" @xaxis label "Atom" @yaxis label "Scd" @TYPE xy There no number. It is like n