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 <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Extracting temperature of specific groups
during the simulations
Message-ID: <167bcf35-f905-9c66-a9d6-e1799132d...@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.mijidd...@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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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