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

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Tue Oct 17 10:57:07 CEST 2017

Is simulated annealing carried out during NPT or in the production run?


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 20 September 2017 03:20
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Running MD simulations at a particular temperature

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

jalemkul at vt.edu | (540) 231-3129


Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list