[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 17 17:37:17 CEST 2010
rasoul nasiri wrote:
> Dear Justin,
> Hello again
> Thanks for the message. I want to increase the distance between solutes
> in simulation box before MD simulation. How can I do it?
You can't. If you know you need a certain distance, that should be part of your
planning :) I suppose you could run a pulling simulation to separate your two
species, but that requires substantially more work (and setup considerations)
than the two or three quick editconf commands to properly build the system.
> On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> rasoul nasiri wrote:
> Dear All,
> I understand one can adjust distance of between solvent
> molecules by genbox command and -vdwd but I don't know, how do
> it between the solutes?
> Position your solutes using editconf -center, then add solvent.
> Thanks for helping!
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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