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

[Mark Abraham]

Hi,

That's your question as part of your experimental design. Why do you want
to do simulated annealing?

Mark

On Tue, Oct 17, 2017 at 10:57 AM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> Is simulated annealing carried out during NPT or in the production run?
>
> Akash
>
> -----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
>
> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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