[gmx-users] How to obtain structures with large RMSD?
liu4gre at gmail.com
Mon Oct 10 17:19:08 CEST 2011
Will the constrain help?
On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <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
> 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
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