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

From: Vlad Cojocaru <>
Date: Tue, 29 Oct 2013 16:53:11 +0100

Thanks Jason, Thanks Daniel,

I was indeed talking only about ptraj processing .. Simulation is run
already .. 150 ns = 50000 frames.

Of course, I understand that its only one matrix to diagonalize
regardless of the number of frames .. However, processing 8K frames
versus 40K frames does make a huge difference in ptraj. with 8K frames
my job was done ovenight (8-9 hours), whereas when I submitted the same
job with 40 K frames, after 2 days I was processing only about 25 % of
the frames. So, the bottleneck is not in the digonalization, but I guess
in the generation of the matrix ...

I will switch to cpptraj ... I used ptraj initially just because does it ..


On 10/29/2013 04:05 PM, Jason Swails wrote:
> 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

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Tue Oct 29 2013 - 09:00:03 PDT
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