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

[Thanh Le]

> 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.
I used 1,000,000 steps for EM (I have always assumed 1,000,000 step to be
2ns)
> potential E of nearly -2.25e-7.

>Check your exponent :)  Surely your system does not have an energy of
(effectively) zero.
You are correct. Hahahaha. I didnt even the error. My potential E is
actually -2.25e-7. Is that a good number?

> 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?
The observable of interest? Do you mean temperature and density by it?
I am still running it and it has been runing over 4 days (nvt run) on my
mbp.
> 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.
I will talk to my sysadmin about it.
Thanks,
Thanh Le