[gmx-users] Using thermostats to create temperature gradient in system

Justin Lemkul jalemkul at vt.edu
Mon Apr 27 02:00:57 CEST 2015

On 4/26/15 7:07 PM, Agnivo Gosai wrote:
> Hello Users,
> This is in relation to my previous posts.
> I am looking to replicate the figure below :
>>   tempgradient.png
> <https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web>
>> Basically I am following this paper for my work :
>>   Lervik_ProtWatInterHT_2009.pdf
> <https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web>
>> Look at figure 6 of the paper.
> My system has water at 300 K and protein at 400 K. The authors of the paper
> describe that they removed the thermostat from the protein and let it relax
> keeping the solvent (water) at 300 K.
> But if I remove thermostat , I get GROMACS error and using freeze groups I
> am not getting any temperatures as the molecules are not moving.

You'll have to show us what you're doing to "get GROMACS error" (what error? 
what were your input settings? Don't make us guess!)

Freezing groups means they have no temperature and they don't move.  This 
certainly isn't what you want.

> I can not understand how to model this system. Any suggestions will be
> helpful. I am doing a literature search but till now it is not fruitful.

Setting tau_t = -1 for the protein tc-grp will "remove" the thermostat; e.g. not 
couple it.  This sounds like what you want.



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


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