AMBER Archive (2006)

Subject: Re: AMBER: use_pme=0 problem

From: David A. Case (case_at_scripps.edu)
Date: Wed May 24 2006 - 19:33:53 CDT

On Wed, May 24, 2006, luckyang_at_gmail.com wrote:
>
> I have identified the source of the difference. The main difference comes
> from the EVDW term. How does use_pme affect VDW energy? In attachment please
> find the file contains the differences.

My best guess is the the longrange vdw correction term is a part of the "PME"
code, so that you are getting this in one calculation but not the other.
Try setting vdwmeth=0 in both runs to see if you get the same results.

I don't know if your force field was parameterized assuming such a long range
correction or not. Leaving it out would lead to a slight change in the
density of the system, but it would depend on the force field to know which
one is "better".

...dac

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