Hi,
You can run the tests in $AMBERHOME/test/jar and $AMBERHOME/test/jar_multi
in order to check it.
On Mon, Jun 27, 2011 at 5:14 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thanks Adrian,
>
> I run sander as per your suggestion ntpr=1, ntwx=1, ntwr=1
>
> sander -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst -r
> smd.rst -x smd.mdcrd
>
> I still get segmentation fault. The output file is attached.
>
> I don't recall getting any error messages during installation. Can you
> please point to me how to check jar?
>
> Thanks again
>
> George
>
>
>
>
>
>
> On Jun 27, 2011, at 10:58 PM, Adrian Roitberg wrote:
>
> > Hi,
> >
> > a couple of things to try.
> >
> > Set nstlim to 100 and
> > ntpr=1000, ntwx=1000, ntwr=5000
> >
> > all to 1 or 10, so you have a fighting chance to see something in the
> > output.
> >
> > Second (perhaps first!): do the jar tests cases pass ?
> >
> > Adrian
> >
> >
> > On 6/27/11 10:40 PM, George Tzotzos wrote:
> >> For both cases:
> >>
> >> 1. sander -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop -c prod.rst
> -r smd.rst -x smd.mdcrd
> >>
> >> 2. mpirun -np 12 sander.MPI -O -i smd.in -o smd.out -p
> 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd
> >>
> >> I get a smd.out which I'm attaching for diagnostics.
> >>
> >> Best regards
> >>
> >> George
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Jun 27, 2011, at 10:06 PM, Dmitry Nilov wrote:
> >>
> >>> Hello,
> >>> I am not sure that it is possible to perform SMD by pmemd. Try to use
> >>> sander.MPI instead of pmemd.MPI.
> >>>
> >>> On Mon, Jun 27, 2011 at 9:49 PM, George Tzotzos<gtzotzos.me.com>
> wrote:
> >>>> Hi everybody,
> >>>>
> >>>> I've just completed a 10ns production run of a protein-ligand complex.
> I would like to study the dissociation of this complex and fI thought that
> SMD would be suitable for this purpose. I tried to repeat the process
> described in the Amber 11 manual as well as in this website (
> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/).
> >>>>
> >>>> I've started sander from a directory containing the solvated prmtop
> file, the trajectory from the production run and a distance restraint file.
> >>>>
> >>>> When I run
> >>>>
> >>>> mpirun -np 12 pmemd.MPI -O -i smd.in -o smd.out -p
> 2wc6_bom_solv.prmtop -c prod.rst -r smd.rst -x smd.mdcrd
> >>>>
> >>>> I get
> >>>>
> >>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> >>>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> >>>>
> >>>> smd 2wc6-bombykol
> >>>> &cntrl
> >>>> imin=0,irest=1,ntx=5,
> >>>> nstlim=500000,dt=0.002,
> >>>> ntc=2,ntf=2,
> >>>> cut=8.0, ntb=2, ntp=1, taup=2.0,
> >>>> ntpr=1000, ntwx=1000, ntwr=5000,
> >>>> ntt=3, gamma_ln=2.0, ig=-1,
> >>>> temp0=300.0,
> >>>> jar=1,
> >>>> /
> >>>> &wt TYPE='DUMPFREQ', istep1=1, /
> >>>> &wt TYPE='END', /
> >>>> DISANG=dist.RST
> >>>> DUMPAVE=dist_vs_t
> >>>> LISTIN=POUT
> >>>> LISTOUT=POUT
> >>>>
> >>>> and the distance restraint dist.RST
> >>>>
> >>>> # Change distance restraint between atoms
> >>>> &rst iat=1533,2223, r2=2.0, rk2=1.0725, r2a=8.0 /
> >>>>
> >>>> where 1533 and 2223 are atom numbers derived from the pdb file.
> >>>>
> >>>> Any help would be much appreciated.
> >>>>
> >>>> Regards
> >>>>
> >>>> George
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Dmitry Nilov
> >>> Faculty of Bioengineering and Bioinformatics,
> >>> Lomonosov Moscow State University
> >>> web: http://enzyme.fbb.msu.ru/
> >>>
> >>> _______________________________________________
> >>> 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
> >
> > --
> > Dr. Adrian E. Roitberg
> > Full Professor
> > Quantum Theory Project, Department of Chemistry
> > University of Florida
> >
> > on Sabbatical in Barcelona until August 2011.
> > Email roitberg.ufl.edu
> >
> > _______________________________________________
> > 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
>
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Mon Jun 27 2011 - 15:00:04 PDT
