[gmx-users] Re: COM Pulling
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 29 15:41:40 CEST 2012
On 6/29/12 9:38 AM, Raj wrote:
> 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 = ??
These settings are backwards. I'm assuming you're trying to pull the group
"DRG" towards/away from your protein. Therefore, "DRG" is pull_group1 and
whatever your protein reference is pull_group0.
> 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
Specify the group name of whatever these residues are as pull_group0.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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