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

[Justin Lemkul]

On 3/25/20 11:40 AM, Mijiddorj B wrote:
> 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?

Google is your friend...

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090607.html

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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