On Fri, Sep 16, 2016 at 6:40 AM, Pooja Kesari <pkesari88.gmail.com> wrote:
> My production run of 4 ns successfully ended.
>
> If i now define my prod.in as follows keeping all the files (rst files)
> unchanged
> *molecular dynamics production run*
> * &cntrl*
> * imin=0, ntx=5,irest=1,*
> *nstlim=5000000, dt=0.002,taup=2.0,*
>
>
> Will my production run start from the beginning or from 4 ns.
>
>
>
Yes, with "irest=1" flag, you will start from 4ns. But I suggest to look
at manual: http://ambermd.org/doc12/Amber16.pdf (start from page 306)
and try to understand about the option inputs before doing extensive run.
Since you're new to amber, you might want to reproduce the tutorial:
http://ambermd.org/tutorials/#basic_tut
Let us know if there is anything that is not clear.
Hai
>
> *defining this in my production run will execute the r*
>
> On Fri, Sep 16, 2016 at 2:35 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Thu, Sep 15, 2016, Bilal Nizami wrote:
> > >
> > > > Question 2. If in case I have to continue the run , How can I do so?
> > > >
> > >
> > > You can continue run by reading the .rst file of the previous MD run
> > > . Following is the input for it
> > >
> > > *sander*
> > > * -O -i Data_03.in -o Data_03.out -p rec_solvated.top -c Data_02.rst -r
> > > Data_03.rst -x Data_03.mdcrd*
> > >
> >
> > Note that you should also set irest=1 in the &cntrl namelist: this tells
> > the program that you are starting from the end of a previous simulation.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards,
> Pooja Kesari
> Research Scholar
> Department Of Biotechnology
> Indian Institute of Technology Roorkee
> INDIA
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Received on Fri Sep 16 2016 - 11:00:02 PDT
