Re: [gmx-users] The equilibrium before REMD simulations

[Justin A. Lemkul]

ÏéÇ« ¿× wrote:
Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium
each replica at its initial target temperature. So i guess we may do the
followings: First, after the minimization and heating, we use NPT to
equilibrium the density of the system. And then with the same initial
system,equilibrium every replica at their target temperature with NVT
ensemble to avoid the instability during REMD and keep the volume constant
among the replicas. Finally, do the REMD simulations. Is this workflow
reasonable enough and do you have any better guide? Any suggestions will be
greatly appreciated!


Seems reasonable, but I am no REMD expert.  There is certainly ample literature 
for you to read to find a suitable established protocol, or to validate your 
procedure.

-Justin

Best regards! Xiangqian Kong








--- On Mon, 11/14/11, Justin A. Lemkul <jalem...@vt.edu> wrote:

From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] The
equilibrium before REMD simulations To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org> Date: Monday, November 14, 2011, 10:25 PM


ÏéÇ« ¿× wrote:
Dear GMX users, I am puzzled about some technical
details regarding to the
REMD simulation and eager for your generous help. With
the purpose to explore
the additional conformational space of the protein, I
want to employ the REMD
method in Gromacs. However, I noticed that in almost
all of the papers about
REMD, a short equilibrium with NPT or NVT was
performed for each replica
respectively before the final REMD run. But i think
the initial structure of
each replica for REMD run is thus different due to the
respective equilibrium
and may somewhat go against the concept of replicas
which i suppose should
have same initial structures while with different
temperatures. So my
question is whether we should or not perform the NVT
or NPT equilibrium
before REMD simulations BTW and why? BTW, i also want
to know which ensemble

Yes, always equilibrate.  Otherwise, your systems will almost certainly not
be stable.  Position restraints are typically applied to the solute of
interest during the initial equilibration, making initial differences
almost insignificant.

should we use in REMD because some papers use NPT
while others use NVT.

Pressure coupling algorithms frequently break down at high temperature, so
NVT is often used.

-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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--
========================================

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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