[gmx-users] On the ussing of different equilibration protocols in NPT

James Starlight jmsstarlight at gmail.com
Sun Sep 28 13:47:40 CEST 2014

Thank you very much for the suggestion!
How do you think are there any drammatic differences between different
preassure coupling (barostats) methods implemented not only in Gromacs but
in other md packages like amber and namd? What barostat will be better for
memrbane protein simulation ?


2014-09-28 0:44 GMT+04:00 Justin Lemkul <jalemkul at vt.edu>:

> On 9/27/14 3:05 PM, James Starlight wrote:
>> Dear Gromac's users!
>> According to tutorials I've noticed that It's important to use position
>> restrains on the protein (and lipid in case of membrane) during npt
>> equilibration phase. But in my mind the presence of the restrains on some
>> part of the system during introducing to some preassure bath (Which act
>> like piston) should produce alot of errors on the stability of the whole
>> system shouldn't it? Does alternatively Parrinello barostat using in
>> Gromacs has completely different preassure coupling method in comparison
>> to
>> langevins piston (in namd)
> If the reference coordinates are not similarly scaled, then yes, you can
> get artifacts.  But in general, any pressure-related artifacts from
> restraints would pale in comparison to simply starting an unrestrained
> equilibration in a pseudo-crystalline environment built by stacking water
> boxes around the solute.
> Restraints on membranes are rather uncommon and are used mostly in cases
> of very badly behaved systems.  Equilibrating membranes requires a lot of
> unrestrained time.  This is the same reason why the initial frames of a
> simple protein-in-water system are also eliminated.  Despite equilibration,
> the system is still generally not at equilibrium for some time.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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