AMBER Archive (2008)

Subject: Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED)

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Wed Jul 30 2008 - 10:29:47 CDT

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_at_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.
>
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