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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 16 2010 - 12:30:06 PDT
