[gmx-users] Extracting temperature of specific groups during the simulations

[Mijiddorj B]

Dear Justin and Alessandra,

Thank you very much for your prompt response. I saved both velocity and
energy data in every 1 ps.




> ------------------------------
>
> Message: 5
> Date: Wed, 25 Mar 2020 08:43:46 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Extracting temperature of specific groups
>         during the simulations
> Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d19a at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 3/25/20 8:40 AM, Alessandra Villa wrote:
> > HI,
> >
> > On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B <b.mijiddorj at gmail.com>
> wrote:
> >
> >> Dear GMX users,
> >>
> >> I would like to extract the temperatures for specific groups during the
> >> simulations. gmx energy gives the system temperature as a function of
> time.
> >> I also tried to get the temperature of a specific group using gmx traj.
> >> However, the data of gmx traj much lower values of the system
> temperatures
> >> for any groups in the systems. I also tried to extract GROUP.tpr and
> >> GROUP.trr files from original data. Then, I performed rerun for the
> group.
> >> However, these data is more lower than that the data of gmx traj.
> >>
> >> I have two questions if possible please advise me.
> >> 1. Is it possible to make correction for the data of gmx traj?
> > 2. Are there any other methods for this purpose?
> >>
> > The values you get by gmx traj are calculated on the number of frames
> that
> > you have saved in trj file (assuming that you have saved velocities in
> your
> > trajectory file). If you have saved with different frequency the energy
> and
> > trj files, you may get different temperature values since you are
> > calculated the temperature on different set of data.
> > When you performed a rerun, you have to be sure that you save every step
> > (that you have in your original trajectory) in the new generated energy
> > file. Otherwise also here you will end up to calculate the temperature
> on a
> > different set of data.
> >
> > Accounting for these points, you should get comparable results with the
> > different approaches.
>
> The saving interval will only account for a very small difference, one
> that will likely be within the error estimate. The biggest difference in
> the outputs of gmx energy and gmx traj is that gmx traj has no knowledge
> of constraints, so it computes degrees of freedom incorrectly. One can
> recover the proper temperature by scaling the output of gmx traj after
> computing the correct number of (unconstrained) degrees of freedom.


>
Thank you again. I am sorry for further asking.
Can you briefly guide me to compute the correct degrees of freedom? How can
I scaling the output?


Best regards,

Mijiddorj



> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
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> End of gromacs.org_gmx-users Digest, Vol 191, Issue 59
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