[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 <jalemkul at vt.edu> wrote:
> 
>> From: Justin A. Lemkul <jalemkul at vt.edu> Subject: Re: [gmx-users] The
>> equilibrium before REMD simulations To: "Discussion list for GROMACS users"
>> <gmx-users at 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

========================================