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

[Pandya, Akash]

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

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

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