[gmx-users] Temperature in NVT file

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 10 13:54:38 CEST 2012

On 6/10/12 7:46 AM, Shima Arasteh wrote:
> Dear gmx users,
> If i want to simulate the system in Temperature=323 k , am I supposed to change
> the ref-t or gen-t in NVT file?

Both.  The gen_temp parameter generates the velocities according to a Maxwell 
distribution.  The ref_t parameter is what the thermostat tries to maintain.  If 
you generate velocities at some temperature other than what you're trying to 
equilibrate, the thermostat may have trouble and the simulation may crash. 
Perhaps you'd get lucky, but there's no reason to risk it by doing something 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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