AMBER Archive (2006)

Subject: Re: AMBER: use_pme=0 problem

From: David A. Case (
Date: Thu May 25 2006 - 12:56:56 CDT

On Thu, May 25, 2006, wrote:
> I may have to keep the longrange VDW correction term. Does this mean I have
> to turn the PME on? Is there a way to keep the longrange VDW correction
> while turn off the PME? The difference of the computer time is huge with and
> without PME for my systems.

You would have to modify the code so that the vdwmeth correction is called
even when use_pme is set to 0. Maybe someone on the list (e.g. Tom Darden)
will volunteer, but you should not hold your breath.

There should not be a big difference with/without PME. Since all your charges
are zero, you can set up a very coarse PME grid (i.e. small values of
nfft1,2,3), which should minimize the time spent in reciprocal space. Even
with the default values, your timing comment is surprising (unless you are
either using lot of parallel processes, or you have a very large unit cell...)


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to