[gmx-users] How to obtain structures with large RMSD?
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 10 17:20:08 CEST 2011
Liu, Liang wrote:
> Will the constrain help?
Bond constraints? Well, in general, they're useful, and likely necessary at
high temperature to keep your system stable. Please be more specific.
> On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Liu, Liang wrote:
> Hi, all,
> I am trying to use Gromacs to obtain structural ensembles around
> native structures (PDB structures).
> However the simulated structures are always very close to the
> initial one, with RMSD < 0.2.
> I am wondering how to obtain large-RMSD structures? Thanks.
> Large RMSD values would indicate non-native structures, which
> doesn't sound like what you're looking for. If your goal is simply
> enhanced sampling, try REMD.
> 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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> Liang Liu
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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