From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Fri Aug 19 2011 - 12:38:34 CDT
Andrea,
You may find some useful info in the "non-bonded interactions" section of
the NAMD User Guide.
The efficiency of the electrostatic energy calculation, when using PME,
should be fairly insensitive to your choice of cutoff. The main relevance
of the cutoff distance is in the computation of the VdW forces; the larger
the cutoff, the more VdW interactions will need to be computed (and the
slower the simulation will run). But if you decrease the cutoff too much,
then accuracy will suffer. The optimum choice of cutoff may be dictated by
the details of your system and/or the force field you are using.
-Erik
On Tue, Aug 16, 2011 at 4:07 PM, Andrea Holfelder
<andreaholfelder_at_gmx.com>wrote:
> I need a little information about PME Grid Setting .
>
> I am using a default cut off of 12A . Is it a little too high ? Can I cut
> it down a bit further to improve computing time ?
> My Pairlist dist is also set 14A .
>
> PME divides the whole system into a system grid pattern of Electrostatic
> interactions and it means that the entire system/PBC unit cell will be
> considered so does it make a point to still use a cutoff value ?
>
> I read that using a cutoff along with PME grid does not mean the
> disfunctionality of either one. I guess it simpy means that PME grid will be
> set weaker beyond 12A and will be stronger till 12A.
> Am I right ? Can somebody explain me the significance of using PME Grid
> along with setting up a cutoff distance?
>
>
> Any help/information will be great
>
>
>
> -Andrea
>
>
>
-- C. Erik Nordgren, Ph.D. University of Pennsylvania
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