Re: [AMBER] Alternative way to do targeted MD

From: Feng Pan <>
Date: Thu, 18 Oct 2018 18:17:34 -0400

Hi, Xiaoling

You may try the SMD method in NFE module, with the use of RMSD as the
reaction coordinates

for the details of this usage, you can check the manual section 21.6.3 for
the usage of &smd,
and 21.6.2 for the RMSD reaction coordinate


On Thu, Oct 18, 2018 at 2:54 PM Xiaoling Leng <> wrote:

> Hello,
> I want to perform a targeted MD simulation on a membrane protein. However
> it is not supported in the pmemd GPU version. May I ask is there any
> alternative way for doing it using GPU? Or like what other types of
> restraints is available in the pmemd can help to simulate a transition in
> between structures?
> Thanks.
> Xiaoling Leng
> _______________________________________________
> AMBER mailing list

Feng Pan
North Carolina State University
Department of Physics
AMBER mailing list
Received on Thu Oct 18 2018 - 15:30:03 PDT
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