AMBER Archive (2006)

Subject: Re: AMBER: use_pme=0 problem

From: luckyang_at_gmail.com
Date: Fri May 26 2006 - 14:10:19 CDT

I tried with verbose=3 and I find the difference comes from the Evdw:

194c192
< Evdw = -2018.956128965737 

---
>      Evdw                   =       -2018.956128965736
199c197
<      Iso virial             =         707.833349909255
---
>      Iso virial             =         707.833349909257
250c248

I include longrange vdw correction in both cases. In attachment please find
the file contains all the differences.

Thanks,

Lu

On 5/26/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Thu, May 25, 2006, luckyang_at_gmail.com wrote:
>
> > I also tried to use eedmeth=5, but I find that using
> > eedmeth = 5 or 1 gives me slightly different Evdw. From the manual I
> thougt
> > this flag has nothing to do with VDW energy.
>
> Weird.  Again, use the verbose option to split things up.  Do you have a
> different number of pairs?  Is the difference with the vdw long-range
> correction?  As the manual says, the eedmeth=4,5 options were designed for
> non-periodic simulations, so there may be something odd going on when they
> are
> used with ntb=1 (perhaps something related to nbflag and skinnb, that
> control
> nonbonded updates.)
>
> ...dac
>
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