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.
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
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.
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
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Received on Tue May 17 2011 - 06:00:03 PDT
