[gmx-users] Heat capacity of the system

Mark Abraham mark.j.abraham at gmail.com
Mon Jan 29 15:00:13 CET 2018


Rerun should not be doing anything with the velocities, because a
trajectory file does not have all the necessary state to reproduce what the
original mdrun did. (I forget whether we've actually stopped mdrun -rerun
from pretending to, but that's at least the plan.) Calculate your heat
capacities from the data in the original .edr files.


On Mon, Jan 29, 2018 at 6:13 AM Malvika K <malvikak91 at gmail.com> wrote:

> Dear Gromacs Users,
> I used mdrun -rerun to recalculate energies of the system (protein in
> water). However, I notice that the temperature in these regenerated .edr
> files is not the same as the the simulation temperature. So if I were to
> calculate the heat capacity (Cp) of the system using this edr file,
> wouldn't it be incorrect since the temperature used is not at which the
> simulation was performed?
> Any help would be appreciated. Thank-you!
> Best,
> Malvika
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