[gmx-users] Run time for energy minimization, nvt, and npt equilibration

[Justin Lemkul]

On 8/1/16 4:47 PM, Thanh Le wrote:
> Hi guys, I have a question regarding the run time for energy minimization,
> nvt and npt equilibration steps. Currently, I am doing a RNA-protein
> simulation (using ff amber14 and spce water model) in a 10 A octahedron box
> containing almost 400k solute atoms.
> For the energy minimization step, I did it for 2 ns and received a

There is no time in EM, only number of steps.

> potential E of nearly -2.25e-7.

Check your exponent :)  Surely your system does not have an energy of 
(effectively) zero.

> I am also doing 2ns for nvt and npt equilibration steps.
> My question is: is 2ns too long for these steps?

You need to run long enough for the observable(s) of interest to converge.  Have 
they?

> Also another question regarding running simulation on a cluster: do I need
> to install gromacs mpi to run it on parallel? Is it necessary since I read
> in the literature gromacs would use all the available cores to run if I
> dont specify the number of cores.

Depends on the configuration of the cluster, how many cores you intend to use, 
etc.  Everything is here: 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

Consult with your sysadmin for best performance on whatever hardware you have.

-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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