For amber11, scee and scnb have been removed from the &cntrl namelist. They
are specified in the topology file now (and default to scee=1.2 and scnb=2.0
if they are not present there).
HTH,
Jason
On Thu, Oct 13, 2011 at 3:44 PM, Mo Chen <mc842.cornell.edu> wrote:
> Hi Jason,
> Okay. Here is my input file and I used to be able to submit this job on a
> nonlocal computer cluster and it was fine running there.
>
> production
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0= 1.0, ntp = 1,
> taup = 2.0,scee = 1.0,scnb = 1.0,
> ig = 712,
> cut = 8, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 323.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002,
> ntpr = 10000, ntwx = 1000, ntwr = 1000
> /
> &ewald vdwmeth=0 /
> /
> END
>
>
> Best,
> Mo
>
> On Thu, Oct 13, 2011 at 3:40 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > What is line 5 of your MDIN file? (or rather print your whole mdin file
> > here).
> >
> > There's an unsupported namelist variable you're trying to use.
> >
> > HTH,
> > Jason
> >
> > On Thu, Oct 13, 2011 at 3:27 PM, Mo Chen <mc842.cornell.edu> wrote:
> >
> > > Dear Amber users/developers,
> > > I have run into some problems when I used pmemd and pmemd.MPI to run a
> > > simulation. And the error messages are as below. May I ask how I could
> > > solve
> > > this problem? Thank you very much!
> > >
> > > chen.sugar9:~/celf-lbox/celf-bglc$ ./test
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/chen/celf-lbox/celf-bglc/celfbglc_prod_3.in, line 5,
> > > position
> > > 17
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F38E335AF7A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F38E3359AF5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F38E429C1F2 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F38E42115FB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F38E4210D0E Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F38E4252E52 Unknown Unknown
> > Unknown
> > > pmemd 00000000005A84B2 Unknown Unknown
> > Unknown
> > > pmemd 00000000004ED11E Unknown Unknown
> > Unknown
> > > pmemd 00000000004EC109 Unknown Unknown
> > Unknown
> > > pmemd 0000000000402E2C Unknown Unknown
> > Unknown
> > > libc.so.6 00007F38E2FD5EFF Unknown Unknown
> > Unknown
> > > pmemd 0000000000402D29 Unknown Unknown
> > Unknown
> > > chen.sugar9:~/celf-lbox/celf-bglc$ ./test
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/chen/celf-lbox/celf-bglc/celfbglc_prod_3.in, line 5,
> > > position
> > > 17
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F596B17BF7A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F596B17AAF5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F596C0BD1F2 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F596C0325FB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F596C031D0E Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F596C073E52 Unknown Unknown
> > Unknown
> > > pmemd.MPI 000000000062278F Unknown Unknown
> > Unknown
> > > pmemd.MPI 000000000050EF19 Unknown Unknown
> > Unknown
> > > pmemd.MPI 0000000000508B99 Unknown Unknown
> > Unknown
> > > pmemd.MPI 000000000042031C Unknown Unknown
> > Unknown
> > > libc.so.6 00007F596ADF6EFF Unknown Unknown
> > Unknown
> > > pmemd.MPI 0000000000420219 Unknown Unknown
> > Unknown
> > >
> >
> --------------------------------------------------------------------------
> > > mpirun has exited due to process rank 0 with PID 23582 on
> > > node sugar9 exiting without calling "finalize". This may
> > > have caused other processes in the application to be
> > > terminated by signals sent by mpirun (as reported here).
> > >
> >
> --------------------------------------------------------------------------
> > >
> > >
> > >
> > > Best,
> > > Mo Chen
> > > Graduate Student
> > > 120 Stocking Hall
> > > Cornell University
> > > Ithaca, NY 14850
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 13 2011 - 13:00:06 PDT
