The instantaneous temperature, to my knowledge, is just calculated as the
average kinetic energy of all of the particles (using the masses and
velocities) scaled by kB and the number of degrees of freedom. There are
some minor tricks used to get the velocities from the leap frog scheme, so
you will probably not be able to do this calculation by hand from the
velocity output (same goes for the potential energy though).
It should be noted that there are TWO input temperatures, tempi and temp0.
The first is only used when velocities are not read from inpcrd and defines
the distribution from which random velocities are drawn. The second one is
a thermostat parameter and only affects the force calculation and/or
velocity updates.
Hope that helps,
Brian
On Thu, Jul 10, 2014 at 4:04 PM, Arthur Roberts <audie.uga.edu> wrote:
> Hi, All,
>
> How is temperature in Amber simulations calculated in the output? I
> have a highly distance restrained system and the temperature is a lot
> lower than the input temperature. From this, I imagine that it is
> calculated using the velocities, but I am not sure. Below is an example
> of the output.
>
> NSTEP = 9800 TIME(PS) = 9.800 TEMP(K) = 16.06 PRESS
> = 0.0
> Etot = -43872.0424 EKtot = 967.0682 EPtot =
> -44839.1106
> BOND = 799.4533 ANGLE = 2653.2592 DIHED =
> 12042.8811
> 1-4 NB = 4164.1652 1-4 EEL = 53895.0746 VDWAALS =
> -10988.7877
> EELEC = -92473.1031 EGB = -15270.6019 RESTRAINT =
> 338.5487
> EAMBER (non-restraint) = -45177.6593
>
> The input temperature here is about 400K. Thank you in advance.
>
> Much appreciated,
> Audie
>
> --
> Dr. Arthur "Audie" Roberts, Ph.D.
> University of Georgia
> Department of Pharmaceutical and Biomedical Sciences
> 240 W. Green St.
> Pharmacy South, Room 424
> Athens, GA 30602
> email: audie.uga.edu
> alt: aroberts99163.yahoo.com
> office: 706-542-7787
> lab: 706-542-5979
> fax: 706-542-5358
> cell: 206-850-7468
> skype=aroberts92122
> For urgent matters, text me at 206-850-7468.
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
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Received on Thu Jul 10 2014 - 14:00:02 PDT
