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

[Alessandra Villa]

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.

Best regards
Alessandra



> Best regards,
>
> Mijiddorj
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