FW: [gmx-users] About Temperature Calculation

Xavier Periole x.periole at chem.rug.nl
Thu Apr 1 16:07:01 CEST 2004

Ane Xu wrote:

>Dear XAvier:
>    No solvent, no temperature coupling, 
No solvent: not good for a good control of temperature.
No temperature coupling: you need a equilibration periode where you
actually control the temperature till it reaches the value you want. In
NVE the E=Epot+Ecin, the equilibration in needed for the equipartition
of the Epot and the Ecin that will (in theory) be conserved for the rest
of the simulation.
What is happening is that the Ecin you give to the system is transformed
into Epot and this will be as long as the equipartition is not reached 
at the
temperature you want.
I would try Stochastic Dynamics. It is probably the best for what you
(I presume) want to do.

>just a NVE simulation with
in your file you have gen_temp = 500  !!! That explains why you have a 
temperature of 500 K

>    Thanks.
>    BTW: why can not I reply the mail with attachment?
I got the attachment !



   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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