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
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?
On Mon, Jan 29, 2018 at 7:29 PM, Mark Abraham <mark.j.abra...@gmail.com>
> 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 <malvika...@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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