Liu, Liang wrote:
Thanks.
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.
-Justin
On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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
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Best,
Liang Liu
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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