[gmx-users] Re: COM Pulling

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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