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

[Justin Lemkul]

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.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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