On 2/2/18 7:10 AM, Malvika K wrote:
I have another query.

I have a protein in water system simulated at different temperatures and I
wish to calculate the heat capacity of the system. Unfortunately, at some
temperatures, I do not have the original .edr files.
In search of a way around this problem, I am wondering if I can use mdrun
-rerun to calculate the energies, extract the enthalpy and calculate Cp
using a script.
I checked this possibility for a temperature at which I do have the
original edr files. The Cp calculated by gromacs is  120.3 J/mol K. I also
used mdrun -rerun for the whole system and extracted enthalpy from the
output file.
The Cp calculated by the script is 82.2 J/mol K. I noticed that the
enthalpy values in the 2 files are quite different : -504693.187500 kJ/mol
(original edr) and -532618.500000 kJ/mol (via mdrun -rerun option).
The bond, potential/total energy values also differ in the 2 log files.

In this case, what would you suggest?

You need to correct the degrees of freedom for any constraints used, and also realize that .edr files contain full energy history so the values produced and corresponding statistics will be different from any quantity you try to recompute from only a subset of the frames in the system.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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