[gmx-users] Re: COM Pulling
Justin A. Lemkul
jalemkul at vt.edu
Sun Jul 1 19:23:23 CEST 2012
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.
> 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.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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