If explicit, you need to set your periodic boundaries (ntb should be 1
or 2) and turn off the implicit solvent model (igb = 0, or better yet
remove igb and gamma_ln completely).
When I was a beginner I found it useful to lay out my input files with
one variable per line. I would then look up each variable and make a
note as to what each one did. Now I think it's even possible to put
fortran-style comments in the input file using the '!' character, e.g.
REM for CpH
&cntrl
icnstph=2, ! Run constant pH in explicit solvent
dt=0.002, ! Time step 2 fs
ioutfm=1, ! Write NetCDF trajectories
...
and so on. Hope this helps,
-Dan
On Wed, Feb 17, 2016 at 8:35 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> Thanks Daniel,
>
> You are right, I didn't check the mdout because I stupidly thought there
> was no output at all. Here is the mdout:
>
> -------------------------------------------------------
> Amber 14 SANDER 2014
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 14
>
> | Run on 02/17/2016 at 15:48:04
>
> | Executable path: pmemd.MPI
> | Working directory: /home/elisa/tutorials/imp_ten_aa/explicit/ph-REMD
> | Hostname: Unknown
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> ph3/ph3.mdin
> | MDOUT:
> ph3/chain.solv10.ph.mdout
> | INPCRD:
> ph3/chain.solv10.equil.rst7
> | PARM:
> chain.solv10.parm7
> | RESTRT:
> ph3/chain.solv10.ph.rst7
> | REFC:
> refc
> | MDVEL:
> mdvel.000
> | MDEN:
> mden.000
> | MDCRD: ph3/chain.solv10.ph.nc
>
> | MDINFO:
> ph3/chain.solv10.ph.mdinfo
> |LOGFILE:
> logfile.000
> | MDFRC:
> mdfrc.000
>
>
> Here is the input file:
>
> REM for
> CpH
> &cntrl
>
> icnstph=2, dt=0.002, ioutfm=1,
> ntxo=2,
> nstlim=100, ig=-1, ntb=0,
> numexchg=5000,
> ntwr=10000, ntwx=1000,
> irest=1,
> cut=8, ntcnstph=5,
> ntpr=1000,
> ntx=5, solvph=3, saltcon=0.1,
> ntt=3,
> ntc=2, ntf=2, gamma_ln=10.0,
> igb=2,
> imin=0, tempi=300, temp0=300,
> iwrap=1,
> ntrelax=100,
>
> /
>
>
>
> Note: ig = -1. Setting random seed to 337654 based on wallclock time in
> microseconds and disabling the synchronization of random numbers
> between tasks to improve performance.
> | ERROR: iwrap = 1 must be used with a periodic box!
> | ERROR: use icnstph=1 for implicit constant pH MD!
> | ERROR: Cut for Generalized Born simulation too small!
>
> Input errors occurred. Terminating execution.
>
>
> So ok, I have an input problem. What do I have to change, in order to run
> pH-REMD with EXPLICIT solvent? I tried to merge two Jason's tutorials, but
> apparently without success :)
>
> Elisa
>
> PS. The test was passed!
>
>
>
> On Wed, Feb 17, 2016 at 4:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> If you want to run an individual Amber test in parallel you need to
>> set the DO_PARALLEL environment variable to whatever your MPI run
>> command should be, so:
>>
>> DO_PARALLEL="mpirun -np 15" ./Run.pHremd
>>
>> Make sure your AMBERHOME environment variable is also properly set.
>> Hope this helps,
>>
>> -Dan
>>
>>
>> On Wed, Feb 17, 2016 at 7:53 AM, Elisa Pieri <elisa.pieri90.gmail.com>
>> wrote:
>> > I'm not sure on how I should "run tests", I went to this directory
>> > /home/elisa/amber14/test/cnstph_remd/Explicit_pHREM and ran the command
>> mpirun
>> > -np 16 Run.pHremd
>> >
>> > this is the result (repeated 16 times):
>> > [agachon:05491] [[29828,1],0] ORTE_ERROR_LOG: A message is attempting to
>> be
>> > sent to a process whose contact information is unknown in file
>> > rml_oob_send.c at line 104
>> > [agachon:05491] [[29828,1],0] could not get route to [[INVALID],INVALID]
>> > [agachon:05491] [[29828,1],0] ORTE_ERROR_LOG: A message is attempting to
>> be
>> > sent to a process whose contact information is unknown in file
>> > base/plm_base_proxy.c at line 81
>> >
>> >
>> > On Wed, Feb 17, 2016 at 3:34 PM, Adrian Roitberg <roitberg.ufl.edu>
>> wrote:
>> >
>> >> where you able to run OTHER sander or pmemd multi core files ?
>> >>
>> >> Run some of them as found in the test directory of the amber
>> >> installation. That way we can figure out if this is a problem with
>> >> constant pH or if it is related to amber itself.
>> >>
>> >> Thanks
>> >> adrian
>> >>
>> >>
>> >> On 2/17/16 9:22 AM, Elisa Pieri wrote:
>> >> > Dear all,
>> >> >
>> >> > I'm experiencing problems running pH-REMD on my computer. I have these
>> >> > machine: Intel® Xeon(R) CPU E5-2623 v3 @ 3.00GHz × 16, and I ran
>> >> > simulations using pmemd.MPI with no problems (I have Amber14). Now I'm
>> >> > using this command:
>> >> >
>> >> > mpirun -np 16 pmemd.MPI -ng 8 -groupfile prova.grpfile &
>> >> >
>> >> > Unfortunately, I get this error:
>> >> >
>> >> > Running multipmemd version of pmemd Amber12
>> >> > Total processors = 16
>> >> > Number of groups = 8
>> >> >
>> >> >
>> >>
>> --------------------------------------------------------------------------
>> >> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> >> > with errorcode 1.
>> >> >
>> >> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> >> > You may or may not see output from other processes, depending on
>> >> > exactly when Open MPI kills them.
>> >> >
>> >>
>> --------------------------------------------------------------------------
>> >> >
>> >>
>> --------------------------------------------------------------------------
>> >> > mpirun has exited due to process rank 12 with PID 4994 on
>> >> > node agachon exiting improperly. There are two reasons this could
>> occur:
>> >> >
>> >> > 1. this process did not call "init" before exiting, but others in
>> >> > the job did. This can cause a job to hang indefinitely while it waits
>> >> > for all processes to call "init". By rule, if one process calls
>> "init",
>> >> > then ALL processes must call "init" prior to termination.
>> >> >
>> >> > 2. this process called "init", but exited without calling "finalize".
>> >> > By rule, all processes that call "init" MUST call "finalize" prior to
>> >> > exiting or it will be considered an "abnormal termination"
>> >> >
>> >> > This may have caused other processes in the application to be
>> >> > terminated by signals sent by mpirun (as reported here).
>> >> >
>> >>
>> --------------------------------------------------------------------------
>> >> > [agachon:04981] 7 more processes have sent help message
>> help-mpi-api.txt
>> >> /
>> >> > mpi-abort
>> >> > [agachon:04981] Set MCA parameter "orte_base_help_aggregate" to 0 to
>> see
>> >> > all help / error messages
>> >> >
>> >> > Can you help me?
>> >> >
>> >> > Elisa
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >> --
>> >> Dr. Adrian E. Roitberg
>> >> Professor.
>> >> Department of Chemistry
>> >> University of Florida
>> >> roitberg.ufl.edu
>> >> 352-392-6972
>> >>
>> >>
>> >> _______________________________________________
>> >> 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
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 17 2016 - 08:00:04 PST
