[gmx-users] Running MD simulations at a particular temperature

Justin Lemkul jalemkul at vt.edu
Wed Sep 20 04:20:38 CEST 2017

On 9/19/17 4:25 PM, Pandya, Akash wrote:
> Hi all,
> I want to run my MD simulation at 65 degrees Celsius. The mdp file has a field as shown below:
> ref_t                    = 338.15  338.15                 ; reference temperature, one for each group, in K
> I am wondering whether the simulation has already reached the desired temperature or does it heat up to 65 degrees throughout the course of the simulation? I hope this makes sense.

The answer depends on what you're doing.  If you've set "gen-vel = yes" 
and "gen-temp = 338.15" then you are initializing a simulation with 
random velocities according to a Maxwell distribution at that 
temperature. If your system is at some other temperature and you're just 
trying to use a thermostat to force a change in that temperature, 
there's no real "warming" going on, rather the thermostat is going to 
push the velocity distribution towards the desired temperature.  Warming 
a system is done via simulated annealing options.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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