On Tue, May 17, 2011 at 2:37 PM, siddesh southekal
<siddeshonline.gmail.com>wrote:
> My earlier mail dint get submitted , so i am reposting it-
>
> Thankyou for the reply Prof.Case and Jason
> I checked the mdout file from the run at the heating step , it does not
> contain the timing information etc , has ended abruptly.The .rst file looks
> ok but cannot be used to restart the simulation.
>
Why not? What errors do you get? And when you say "it looks OK", do you
mean you tried visualizing it? Or does it just appear to be 6 columns of
numbers?
> I set a lower limit ntpr=1 and nstlim=10 , the simulation ends without any
> errror , the structure looks stable ( sorry for the mistake previously i
> loaded the .rst file instead of trajectory file ). I can restart this
> simulation
>
> Strangely i observe that the simulation takes much longer time ( 12 hrs for
> 100 ps smulation on 64 cores ) after docking the ligand molecule while i
>
You are sure it's using 64 cores? In amber11, the parallel version of pmemd
is now called pmemd.MPI, whereas in earlier versions of amber it was just
"pmemd". The output file will actually tell you how many cores it's being
run on.
> could run 1ns simulation within a day without the ligand for the same
> system. If it exceeds the wall clock i get the above forrtl:error in the
> standard error file and the .rst file is useless.
> i dont think adding ligand molecule ( 12-15 atoms ) should make such a big
> difference in the simulation time.
>
I would agree with you here.
All the best,
Jason
> thanks,
> Siddesh
>
> On Thu, May 5, 2011 at 3:36 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Thu, May 5, 2011 at 12:07 PM, siddesh southekal
> > <siddeshonline.gmail.com>wrote:
> >
> > > Dear Users ,
> > >
> > > I am trying to run MD of a protein in a lipid environment to which a
> > ligand
> > > molecule is docked using the AutoDock program . I did not have any
> > problem
> > > when i ran MD of the protein in lipid environment without the ligand
> > > molecule .
> > > But i face problems once i dock the ligand molecule into the protein .
> > >
> > > After I minimize the system (ligand-protein complex) and then I try to
> > run
> > > MD in the heating stage , the simulation runs without any problem ( but
> > as
> > > long as the wall clock is given , which should end in much shorter time
> )
> > > and completes without any error in the .out file . The standard error
> > file
> > > consists of the following error . Same error occurs even in
> > > water environment .The .rst file cannot be used again and the
> simulation
> > > gets aborted.
> > >
> > > forrtl: error (78): process killed (SIGTERM)
> > > forrtl: error (78): process killed (SIGTERM)
> > >
> >
> > This tells me that the program received a termination signal. This is
> > either done by using CTRL-C in an interactive terminal, or it's sent by
> the
> > queuing system if you blow past your wall clock time.
> >
> > Try setting a lower time limit to see if it completes, and like Professor
> > Case suggested, set ntpr=1, and nstlim=10.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 17 2011 - 08:00:02 PDT
