[gmx-users] parameters in *.mdp files

[Shima Arasteh]

Thanks for your reply.
Yes, using a better thermostat doesn't mean I have a longer simulation. But, a better thermostat has more ab-initio terms, which I think the calculation of them might be time consuming. That's why I guess I will have a longer simulation ( the time which the computer spends to simulate a system for adjusted time such as 50 ns).


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Sunday, August 19, 2012 5:19 PM
Subject: Re: [gmx-users] parameters in *.mdp files



On 8/19/12 7:39 AM, Shima Arasteh wrote:
> Hi all,
> 
> In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp ,
> npt.mdp or md.mdp are the same. Is it necessary to use the same temperature
> coupling parameters in .mdp files? Generally, which parameters are supposed
> to be the same in .mdp files of a simulation?
> 

The thermostat can change.  Generally, the Berendsen method is advisable for initial NVT equilibration because it allows systems to relax gently.  Starting with Nose-Hoover, for instance, can lead to rapid instabilities and a crash. Once equilibrated, a more rigorous method should be used.

Nearly all .mdp settings are identical for any phase of a simulation (equilibration or data collection).  Most of the settings are dictated by the force field you've chosen, and since that's not changing, neither should your .mdp settings.  The thermostat might be adjusted, as stated above, and restraints removed or applied, tau_t or tau_p may be adjusted as the system reaches equilibrium.  Outside of these settings, everything else is generally static.

> 
> If a more accurate thermostat is used in a simulation, would it increase the
> time of simulation? What kind of simulations worthwhile a more accurate
> thermostats?
> 

You should always use an accurate thermostat.  Using a "better" thermostat does not mean you have to run your simulation longer.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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