Dear Amber users/developers,
May I ask in what way do the wrong scee and scnb affect the dynamics? I have
compared the decomposed energy terms calculated from Amber (setting cut = 8)
as well as CHARMM (using pmewald and vdw atom vswitched by setting ctonnb =
8, ctofnb =8 and cutnb =12), and the decomposed potential energy terms are
basically the same. So I wonder how scee and scnb in amber PMEMD affect the
dynamics. Do they affect the random forces in langevin dynamics? I wonder if
my previous simulation should be trashed since I used the older version and
did not use the default values of scee and scnb. Thank you very much!
Best,
Mo
On Thu, Oct 13, 2011 at 3:46 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 21 2011 - 21:00:02 PDT
