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

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Apr 26 00:36:01 CEST 2015

Hello Users

I have equilibrated a protein solvent system using NVT ensemble and V -
rescale thermostat. Target temperature was 300 K.

Now I want to establish a temperature gradient in my system as follows :

1. Use Two Berendsen thermostats separately for Protein and Non Protein
Protein grp , T = 400 K
Non protein grp, T = 300 K.

Run in NVT for 100 ps.

2. Then remove thermostat from Protein grp. But keep thermostat for Non
Protein grp.
Run in NVT for 500 ps. I hope that the protein will come down or relax to
300 K.

Is the above scheme feasible ? I have not yet tried.

I use COM motion removal for the whole system.

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

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