On Thu, Sep 16, 2010 at 4:05 PM, <mdkvia.yahoo.com> wrote:
> Hi Jason,
>
> Thank you for the reply. I apologize for the confusion with -c. I meant
> -ref.
>
> So my question #2 is: Say I run a single job with -ref option and the
> reference coordinates are in file ref.rst. Now I divide this single job to 3
> as I mentioned in the previous email. So, now for the -ref of the 3 jobs I
> should provide the same ref.rst if I want to have the same results as the
> single long job. Is this line of thinking correct?
>
Like Scott said, they'll never be the "same". However, you'll want to keep
all reference structures the same to get the *equivalent* of a single run,
yes. You should decide what to do based on what you're trying to learn
though, not necessarily whether or not you want to emulate a single long
run.
>
> Yes, I understand that there will be rounding off errors etc. But apart
> from those, the results must be comparable b/w the single long job and the 3
> shorter jobs. If not I was just wondering how to run a long simulation
> without having to deal with unmanageably huge trajectory files.
>
Write out less often (i.e. make ntwx larger). Use ioutfm=1 to write to a
higher precision, compressed binary trajectory format (netCDF) to obtain
smaller trajectories of higher precision that are much faster to read,
write, and process. This is detailed in the amber manual.
Hope this helps,
Jason
> Thank you,
>
> Maal
>
> --- On Thu, 9/16/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Sander/pmemd usage: refc question
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Thursday, September 16, 2010, 3:23 PM
> > Hello,
> >
> > On Thu, Sep 16, 2010 at 3:10 PM, <mdkvia.yahoo.com>
> > wrote:
> >
> > > Dear Amber users,
> > >
> > > I'm new to Amber and I would like to divide a MD job
> > into several subjobs.
> > > So, I intend to invoke sander.MPI (alternatively
> > pmemd) the following way:
> > >
> > > sander.MPI -O -i subjob.inp -o subjob_1.out -c
> > subjob_0.rst -p testjob.top
> > > -r subjob_1.rst -ref subjob_0.rst -x subjob_1.mdcrd
> > -inf subjob_1.inf
> > >
> > > sander.MPI -O -i subjob.inp -o subjob_2.out -c
> > subjob_1.rst -p testjob.top
> > > -r subjob_2.rst -ref subjob_1.rst -x subjob_2.mdcrd
> > -inf subjob_2.inf
> > >
> > > sander.MPI -O -i subjob.inp -o subjob_3.out -c
> > subjob_2.rst -p testjob.top
> > > -r subjob_3.rst -ref subjob_2.rst -x subjob_3.mdcrd
> > -inf subjob_3.inf
> > >
> > > In the subjob.inp file I'll be having ntx=5 and
> > irest=1. My questions are
> > > as follows:
> > >
> > > 1. If the simulation has no restraints (ntr=0), then
> > do I even need to
> > > specify -c option?
> > >
> >
> > -c specifies the input coordinate (inpcrd) file, not the
> > restraint file.
> > The restraint file is specified by -ref . Therefore,
> > -c is ALWAYS required
> > (unless, of course, your input coordinate file is called
> > "inpcrd"). -ref is
> > only required when you specify ntr=1.
> >
> >
> > >
> > > 2. If I do (either because the answer to #1 is yes or
> > ntr=1) then shouldn't
> > > the coordinates for the -c option be same (say
> > subjob_0.rst) for all 3
> > > subjobs (i.e. above usage is wrong)?
> > >
> >
> > Why would they have to be the same? It depends on
> > what you're trying to
> > do...
> >
> >
> > >
> > > 3. Lets say each subjob is 1 ns in length. Would the
> > combination of the 3
> > > trajectories be identical to a single 3 ns job (run
> > with identical options
> > > except for nstlim)?
> > >
> >
> > What do you mean by "identical"? Round-off will make
> > them slightly
> > different for a long enough trajectory. However, it
> > should behave more or
> > less the same as a single long run. The numbers will
> > not likely be
> > "identical" except under strict circumstances. You
> > can always check for
> > yourself, though.
> >
> > Hope this helps,
> > Jason
> >
> > Thank you in advance,
> > >
> > > Maal
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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AMBER.ambermd.org
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Received on Thu Sep 16 2010 - 14:00:03 PDT
