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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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