[gmx-users] on non-equilibrium MD

[Justin Lemkul]

On 4/1/16 10:15 PM, Brett wrote:
> Dear All,
>
> For non-equilibrium MD, does it mean there would be no need for the energy
> minimization step, NVT equilibrium step and NPT equilibrium step before the
> production MD? In which situation we use non-equilibrium MD, and in which
> situation we use the production MD with energy minimization step, NVT
> equilibrium step and NPT equilibrium step?
>

The term "non-equilibrium MD" covers a lot of different possibilities, each with 
their own applications - freezing, applying selective acceleration, pull code, 
etc.  There is no single answer to when these should be applied because they are 
intrinsically different.

Just because there is some perturbing or net force on the system does not mean 
you can skip all the normal preparation steps.  I can practically guarantee that 
if you skip minimization and try to apply the pull code, your system will 
immediately crash.  Some things are always necessary, but the exact protocol 
depends on the goals at hand and the specific technique(s) being applied.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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