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?
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.
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
>
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Received on Thu Sep 16 2010 - 13:30:04 PDT
