Tutorial-l Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Oct 02 2008 - 13:55:04 CDT

Hi,

In the namd tutorial it says on page 24: "         Typically, a grid size slightly less than 1  ̊ is a good
                                                     A
choice to reproduce charge distribution in biological systems,
where the closest atoms have a bond separation on the order of 1
 ̊A. Furthermore, for speed in computing Fast Fourier Transforms,
PMEGridSizeX should be chosen so that it can be factorized by
2, 3, or 5. If your cellBasisVector1 = (60, 0, 0), a good
choice for PMEGridSizeX might be 64, since 60  ̊ A/ 64 = 0.9375
 ̊A and 64 = 26."

While in the namd tutorial they used gridsizes of 32 in each direction when the cellBasisVector was 42, 44 and 47, yet the simulation went OK.

I am asking this as I was running a simulation of cellBasisVector around 35 in each direction, and the gridsizes were set to 32s according to the tutorial. I have been looking for the reasons of the unexpected termination of the simulation. And according to the tutorial this couldn't be one.

* My question is, how far could the PMEGridSizes affect the simulation?
* And if the equilibration step wasn't long enough, could this terminate the simulation before completion?

Thanks
Rabab

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