[gmx-users] PME grid spacing
Justin A. Lemkul
jalemkul at vt.edu
Tue May 11 17:06:01 CEST 2010
> Dear GROMACS experts,
> Initially I wanted to do MD for a stack of hexane molecules. MD showed
> very high repulsion potential. On the recommendation of Justin, I
> simplified the problem and now I have only one Hexane molecule.
> 1- I dont know why I do not get the written pdb files normally generated
> after MD! I want to watch the trajectory.
What files are you talking about? The trajectory file is written in .trr format
(or optionally, .xtc format if you have nstxtcout > 1).
> 2- Could you please kindly take a look at energy values and let me know
> if values are reasonable so that I can proceed to building stack of
> hexane molecules. Pon
Your results are fine. You have a single hexane molecule in isolation so you
may not get a negative potential energy, which is a normal criterion for
> 3- Please help me understand NOTE 2 in output.grompp_md (end of this
> post message)
A lot of this information was unnecessary, and repetitive from your previous posts.
> Estimate for the relative computational load of the PME mesh part: 0.97
> NOTE 2 [file aminoacids.dat, line 1]:
> The optimal PME mesh load for parallel simulations is below 0.5
> and for highly parallel simulations between 0.25 and 0.33,
> for higher performance, increase the cut-off and the PME grid spacing
The error message is quite explicit, but is nothing you need to worry about.
Your system is not one that lends itself to optimization. A single molecule in
isolation does not parallelize very well (nor do you need it to). If you get
this message from a larger system, then you may have some inappropriate
settings, but for now, don't worry.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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