Thanks both Jason and Scott!
--- 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, 4:36 PM
> 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
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> _______________________________________________
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> > > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 16 2010 - 14:30:03 PDT
