[gmx-users] Heat capacity of the system
David van der Spoel
spoel at xray.bmc.uu.se
Sat Feb 3 11:00:44 CET 2018
Den 2018-02-03 kl. 09:13, skrev Malvika K:
> How can I correct the degrees of freedom for any constraints? I used all
> the whole trajectory to calculate Cp for the entire system, with the
> original .edr files and using .edr files calculated using gmx energy and
> notice the difference mentioned before.
> I notice that for the same frame, the bond and potential energies are
> different using the 2 methods, causing the difference in enthalpy and Cp.
my old paper has most of the information you are looking for:
> I am seeking a solution to calculate Cp for the systems for which I do not
> have the original .edr files. Please can you suggest any?
If you have the log files you can script the energy out of it. If not,
rerun the simulations.
> On Fri, Feb 2, 2018 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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
>> jalemkul at vt.edu | (540) 231-3129
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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