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

Agnivo Gosai agnivogromacs14 at gmail.com
Mon Apr 27 01:07:08 CEST 2015

Hello Users,

This is in relation to my previous posts.

I am looking to replicate the figure below :

Basically I am following this paper for my work :

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.

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.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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