Re: [AMBER] Extract temperature of a subsytem

From: <>
Date: Fri, 25 Nov 2016 15:15:53 +0100

  Hi Gustavo,
Thanks for your answer.

Yes, I've saved the velocities. Yes, I know I can do that, but the
format of the velocity files is quite difficult to manage (10
columns), and besides I would have to extract the masses from
somewhere else.

I can extract the velocities of the subsystem of interest with
cpptraj, but the format is still the same one (not very friendly).

  It can be done, of course, but I was wondering if there's already
some tool implemented in AMBER allowing me do to this without having
to waste time writing a program to read the velocities in that
awful-looking format and the masses to compute the Kinetic energy.


Quoting Gustavo Seabra <>:

> Have you saved the velocities? AFAIK, the are not saved by default
> except on the restart file. Assuming you have the velocities, you
> can calculate the temperature by first calculating the kinetic
> energy, then using T=2*KE/(3*k), where k is Boltzmann constant.
> —
> Gustavo Seabra.
>> Em 25 de nov de 2016, à(s) 08:22, escreveu:
>> Hi, I 've run some simulations and I'd like to be able to extract
>> the instantaneous temperatures of just some of the residues. Is there
>> a quick way to achieve this? Like a flag with a mask or something? Or
>> do I have to do all the hard work processing the output files (not
>> much of a problem, but still, it would be nice if there was a quick
>> way to accomplish this)?
>> Thank you
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Received on Fri Nov 25 2016 - 06:30:02 PST
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