[gmx-users] Heat capacity of the system

[Malvika K]

Okay.
Thank-you.

On Sat, Feb 3, 2018 at 3:30 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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:
> http://pubs.rsc.org/en/Content/ArticleLanding/2008/CP/
> b716554d#!divAbstract
>
>
>> 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.
>
>
>
>> Thanks,
>> Malvika
>>
>> 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
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>
> --
> 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.
> http://www.icm.uu.se
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>