[gmx-users] Temperature in NVT file

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jun 10 18:50:10 CEST 2012

Thanks for your reply.
So if I have to simulate the system at T=323 K , I need to set both ref-temp and gen-temp at 323K. Right? I guess no difference between two items , I mean ref and gen, to be set at what temperature!


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, June 10, 2012 4:24 PM
Subject: Re: [gmx-users] Temperature in NVT file

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 nonsensical.


-- ========================================

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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