On Wed, Apr 13, 2011 at 2:23 AM, Sanjay kundu <sanjay.kundu4.gmail.com>wrote:
> 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.
>
If they are for gas phase, then ntb should be 0 and cut should be large.
Note you can also use implicit solvent models (GB or PB).
--Jason
>
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks and Regards,
> 'Sanjay Kundu'
> Mb.No:9540532962
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 13 2011 - 09:30:06 PDT
