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

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Apr 26 23:56:35 CEST 2015

Hello users,

Thanks a lot Suzen for an insightful suggestion. My protein and solvent
have been equilibrated at 300 K in an NVT ensemble.

I raised the temperature of protein gradually by using simulated annealing
to 400 K and the solvent has been kept at 300 K.

Now I wish to get a temperature gradient such that the temperature of the
protein comes down by exchanging heat with the solvent to 300 K.

So as per your suggestion , do I need to freeze the solvent group so that
its position will not be updated and hence it will have the same
temperature ??

For the protein if I do not use a thermostat , GROMACS will give error
message. So how do I fix this problem ?

Or, should I freeze the protein instead and use a thermostat on the solvent

I am trying both of these as I write this mail.

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

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