[gmx-users] Re: COM Pulling

[Justin A. Lemkul]

On 7/1/12 12:02 AM, Raj wrote:
> Dear Justin,
>
> I've tried what you have suggested. I have used the pull code and gave 4
> amino acid residues as a reference group. The location of the groups are one
> below the ligand (in the protein core) and 3 were on the above ( towards the
> active site gorge). When i used the code
>

This sounds like a poor approach.  If you have some residues that are internal 
and some that are external, mdrun won't do any productive pulling.  Define one 
group in a concerted area as a reference group and pull with respect to it to 
move the ligand.

-Justin

> pull                 = umbrella
> pull_geometry  = distance  ; simple distance increase
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = DRG
> pull_group1     = reference groups
> pull_rate1       = 0.003      ; 0.01 nm per ps = 10 nm per ns
> pull_k1           = 1000      ; kJ mol^-1 nm^-2
>
> the ligand migrated more and more towards the protein , not coming out of
> the protein through the channel i defined by referring the amino acid groups
>
> when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and
> pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can
> not be zero.
>
> when i was trying to use pull_geometry = direction the system blowed up. but
> the pull_geometry = distance worked well.
>
> please give me a suggestion to resolve the issue
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998989.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
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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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