[gmx-users] Re: COM Pulling
princecrusial05 at gmail.com
Fri Jun 29 15:38:51 CEST 2012
Thanks for your reply Justin.
>From your umbrella tutorial I thought the reference group should be the
protein. Now from your reply i think I can specify any amino acid residue in
the protein and I can drive the ligand towards the residue.
where I need to specify the group
If i'm using the pull code
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DRG
pull_group1 = ??
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
how can i specify the residue if i want to pull towards the direction of 3
amino acids, and I've included in the index file
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