Just to update those interested,
I compared the namdenergy/vmd results with the results I got using
mm_pbsa.pl scritp (gas phase energy) for my waterbox (TIP3P)
simulation and they matched perfectly.
I took me a while until I realized that I had and wrong index in the
LJ B coeff. Now, everything is ok.
Thanks for all contributions,
--alessandro
On Sat, Jul 26, 2008 at 6:46 PM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> I don't think Alessandro used Amber for energies, and if it's a simple program
> it probably is non-periodic. I think it's likely the 1-4 scaling factor for vdw.
> one of them ( can't recall, Adrian may know) either ele or vdw has the
> wrong 1-4 scaling in NAMD for amber ff.
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Aug 03 2008 - 06:07:12 PDT
