From: Naveen Michaud-Agrawal (
Date: Thu Feb 24 2005 - 16:02:10 CST

Hi, I realized that one of my grid sizes does not have integer factors of
2,3,5. My z grid size hovers around 90 angstroms (I'm doing a constant
area simulation). Is there a problem if I change the PMEGridSize in the
middle of the simulation from 132 (this was from a previous simulation) to
96? I'm sure the energetics will change slightly since there will be less
sampling points, but the speedup is sizable.


Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

On Thu, 24 Feb 2005, Marcela P.Aliste wrote:

> Hi:
> I used NAMD before:
> I change to AMBER topology to calculate protein-RNA interaction.
> The problem is with the water model TIP3, that AMBER generate the third
> bond, but there are not
> definition for angle. I tried 2 fs time step using SHAKE algorithm, and
> the simulation crush after 1 step.
> I changed to 1 fs without using SHAKE. it is running. but it will take
> twice the time.
> How can I fix this problem using AMBER & shake.
> Thanks
> M. Aliste

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