Hi Ross,
By now I have checked my topology and coordinate file and both are for a gas
phase. I am not getting any output at all since the 'sander' process is
running endlessly without printing any data in the 'md_classical.out' file
and also have set the cut-off value to 8 and ntb=1 will be appropriate i
guess.
On Wed, Apr 13, 2011 at 4:01 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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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>
--
Thanks and Regards,
'Sanjay Kundu'
Mb.No:9540532962
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Received on Wed Apr 13 2011 - 02:30:05 PDT
