[gmx-users] Running MD simulations at a particular temperature
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users