AMBER Archive (2006)

Subject: Re: AMBER: use_pme=0 problem

From: luckyang_at_gmail.com
Date: Wed May 24 2006 - 19:51:10 CDT

Dear Dr. Case,

Thank you very much for your help. It gives me the same results if I set
"vdwmeth = 0". I will check the TraPPE paper for the right option of these
flags.

All the best.

Lu

On 5/24/06, David A. Case <case_at_scripps.edu> wrote:
>
> 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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