Thank you David.
I have just changed my executable from pmemd.MPI to sander.MPI.
This resulted in a fairly obvious error: Must have more residues than processors. As I have only 3 molecules in this test case then in retrospect I would have expected this. Nevertheless this error did not show up on the pmemd.MPI run.
I then ran the job in serial mode sander and low and behold have 'jiggling' molecules.
So does this mean I have not compiled pmemd.MPI correctly or should pmemd.MPI produce the same error as sander.MPI and crash?
Steve
Dr S Bailey
Department of Physics
Lancaster University UK
Email: s.bailey.lancaster.ac.uk
Tel: +441524592844
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: 18 June 2013 14:56
To: AMBER Mailing List
Subject: Re: [AMBER] PEG
On Tue, Jun 18, 2013, Bailey, Steven wrote:
>
> Setting up a complex of a number of PEG chain linked units I then run
> antechamber to obtain charges and input files.
> The MD simulation uses igb=1.
> After equilibrating to 300K I examine the MD output and the molecules
> show no interaction i.e. they seem to be frozen with no twisting and
> no vdW nor charge interactions. When running using a Dreiding force
> field for example in other MD packages there is a great deal of
> interaction. Can anyone advise what might be going wrong or would this
> be expected using the Gaff force field.
Are you sure the only difference between the two simulations (GAFF vs
Dreiding) is the force field? The qualitative behavior of MD should be the same. Did you run both calculations in the same program, with the same settings? It is very hard to get much insight from your short description, but it sounds more like a thermostat problem than a force field problem.
...dac
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Received on Tue Jun 18 2013 - 07:30:02 PDT
