Re: [AMBER] huge values for the vibrational entropy from ptraj

From: Jason Swails <>
Date: Tue, 29 Oct 2013 11:05:29 -0400

On Tue, Oct 29, 2013 at 9:50 AM, Vlad Cojocaru <> wrote:

> yes, this was a test with 8000 frames ..
> The complex has 6353 atoms
> The receptor has 3788 atoms
> The ligand has 2565
> My trajectory has in total 50000 frames .. I wanted to exclude the first
> 10000. So I'd be left with 40000 frames .. This would make about
> 6*Natoms of the largest system. However this is extremely expensive for
> a 1 core job ...
> Maybe I could give it a try with the parallel ptraj.

I don't understand here, are you talking about the original simulation with
sander/pmemd or analyzing 40K frames with ptraj? From the sounds of it,
you're talking about ptraj? Parallel ptraj will be of no help here (I
don't think this action is even parallelized, anyway).

With a quasi-harmonic approximation you are creating and diagonalizing only
ONE matrix, regardless of how many frames you use. Using 40K frames in a
quasi-harmonic analysis vs. 8K frames will not make a huge difference to
the processing time, I don't think.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Oct 29 2013 - 08:30:04 PDT
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