[gmx-users] high-temperature MD

[Justin Lemkul]

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
>>
>> 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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>

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

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

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