Ya it is same for PMEMD and SANDER
On Mon, May 19, 2014 at 11:55 AM, sammia khatak <saammia_kt.hotmail.com>wrote:
> I am working in sander, will it work for this as well.
>
>
> > Date: Mon, 19 May 2014 11:35:10 +0200
> > From: bhakatsoumendranath.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] sander restart
> >
> > It means it left 5000-3050=1950 steps to be completed
> > Now in the input file put
> >
> > min.in
> > energy minimization stage 2
> > &cntrl
> > imin=1, maxcyc=1950, ncyc=2500,
> > cut=10.0, ntb=1,
> > ntc=1, ntf=1,
> > ntpr=10,
> > ntr=1,
> > restraintmask=':1-500',
> > restraint_wt=2.0
> > /
> >
> > suppose your output is min1.out and restrat file is min1.rst then in the
> > submission file edit like this
> >
> > $AMBERHOME/bin/pmemd -O -i min.in -o min2.out -p com_solvated.top -c
> > min1.rst -r min2.rst
> >
> > All d best!!
> >
> >
> > On Mon, May 19, 2014 at 11:25 AM, sammia khatak <saammia_kt.hotmail.com
> >wrote:
> >
> > > min.in
> > > energy minimization stage 1
> > > &cntrl
> > > imin=1, maxcyc=5000, ncyc=2500,
> > > cut=10.0, ntb=1,
> > > ntc=1, ntf=1,
> > > ntpr=10,
> > > ntr=1,
> > > restraintmask=':1-500',
> > > restraint_wt=2.0
> > > /
> > > In min.out it shows last run as 3050 where should i bring changes in
> order
> > > to implement your suggestion.
> > >
> > >
> > > > Date: Mon, 19 May 2014 09:28:58 +0200
> > > > From: bhakatsoumendranath.gmail.com
> > > > To: amber.ambermd.org
> > > > Subject: Re: [AMBER] sander restart
> > > >
> > > > use the restart file generated and check in how many steps the md or
> > > > whatever finished. Changed the remaining number of steps in the
> input and
> > > > re-run from the restart file.
> > > > All d best!!
> > > >
> > > >
> > > > On Mon, May 19, 2014 at 8:57 AM, sammia khatak <
> saammia_kt.hotmail.com
> > > >wrote:
> > > >
> > > > > Hello
> > > > > Is there a way to restart calculation in sander when it stops due
> to
> > > > > powerout problem from the point where system switched off.
> > > > > Thanks
> > > > >
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> > > >
> > > >
> > > >
> > > > --
> > > > Thanks & Regards;
> > > > Soumendranath Bhakat
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> >
> >
> >
> > --
> > Thanks & Regards;
> > Soumendranath Bhakat
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon May 19 2014 - 03:30:02 PDT
