[gmx-users] Heat capacity of the system
malvikak91 at gmail.com
Mon Feb 5 05:19:34 CET 2018
On Sat, Feb 3, 2018 at 3:30 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> 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
>>>> temperatures, I do not have the original .edr files.
>>>> In search of a way around this problem, I am wondering if I can use
>>>> -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
>>>> 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
>>>> (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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