[gmx-users] PME grid spacing

Justin A. Lemkul jalemkul at vt.edu
Tue May 11 17:06:01 CEST 2010

Moeed wrote:
> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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