Hi Sanjay,
It would be useful to know where in the output it stopped. Did you get no
output at all or did sander produce some output and then stop before
printing the step 0 energies?
My guess is that you are trying to run a periodic boundary calculation
(ntb=1) but your topology and coordinate file are for a gas phase (or
solvent cap) system.
Additionally as a point of note you are running with a cut off of 20.0 but
are using periodic boundaries. In this case your long range electrostatics
are handled by the Particle Mesh Ewald algorithm and therefore a cutoff of
8.0 is fine and will give you much better performance.
All the best
Ross
> -----Original Message-----
> From: Sanjay kundu [mailto:sanjay.kundu4.gmail.com]
> Sent: Monday, April 11, 2011 10:53 PM
> To: amber.ambermd.org
> Subject: [AMBER] Error on running parameter 'sander'
>
> Sir/Mam,
> I have been running '*A Coupled Potential QM/MM Simulation*' in Amber9
> for
> my project work in Neuraminidase protein of H1N1. Starting from initial
> steps, the parameter was successfully run till 'Classical MD' i.e.
> min_classical.in using sander. But on step 'md_classical.in' the sander
> is
> running endlessly without giving any output. The maximum time I waited
> for
> result was 2 days. Hereby, I have attached the script file for running
> sander i.e. 'md_classical.in' file. Will be thankful to you for a
> positive
> reply.
>
> --
> Thanks and Regards,
> 'Sanjay Kundu'
> Mb.No:9540532962
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Received on Tue Apr 12 2011 - 16:00:03 PDT
