[gmx-users] Re: COM Pulling

Raj 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

please help...

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