[gmx-users] About Temperature Calculation

Xavier Periole x.periole at chem.rug.nl
Thu Apr 1 16:44:00 CEST 2004

Ane Xu wrote:

>     So, the 0K equilibrium potential (what I got from "em") is not the
>"quilibrium" one in the 300K or 500K case, 
Minimization is without temperature. So no, after minimization the Epot 
is not at
all the "one" you would expect to be at 300K or 500K. Note that Epot at 
300 and
500 would be very different.

>and if I wanna got a system
>at 300K, the only way is to do "SD" or "MD" with higher initial
>temperature (which results in a equilibrium 300K state). Is it right?
SD is a way to get rid of artefact due to the absence of solvent. I am 
not a specialist
of it but it seems to work well.
Give a higher temperature to reach the one you want is not the best 
solution. The
energy you would give would be too high. In general you do it in several 
where the system got a chance to "relax" at each temperature: 0, 50, 
100, 150,
200, 250, 300 K for ex. But in vacuum will not work very good.

SD seems a better solution.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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