[gmx-users] high-temperature MD

Christopher Neale chris.neale at alum.utoronto.ca
Thu Oct 6 20:27:40 CEST 2016


Depends, actually. There are reasons one might want to simulate a system at 380 K in NVT using the average box volume from the 300 K NPT simulation. Temperature replica exchange typically employs NVT and so might other temperature-based enhanced sampling approaches. Justin's right, you have to think it through, but I'm just chiming in to suggest that the answer is not obvious from this thread thus far. TIP3P water doesn't boil in NPT until somewhere around 550 K, so NPT at 380 K is certainly possible.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 06 October 2016 09:34:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] high-temperature MD

On 10/6/16 8:54 AM, OuyangYanhua wrote:
> Dear Justin,
>>
> I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD.
> The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the same as the 300k, which means the 380k is also first equilibrated at NVT, then at NPT and production MD at NPT ensemble.
>

Think scientifically.  If you only want to vary the temperature, does it make
any sense to vary the simulation protocol?

-Justin

> Best regards,
> Ouyang
>
>> 在 2016年10月6日,下午7:22,Justin Lemkul <jalemkul at vt.edu> 写道:
>>
>>
>>
>> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we
>>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>>> production MD at NPT ensemble normally. Does someone know whether the 380K-MD
>>> can only  perform at NVT ensemble since the temperature(380K) is a high
>>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>>>
>>
>> 380 K is not very high.  What you choose to do needs to be based on whatever real-world conditions you want to model.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
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--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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