Alan,
Even it is 'solves' the problem, it really does not.
TIPnP models ARE rigid. The parameters and warranty only hold under
rigid conditions. SO, if you simulate them with a smaller dt, they do
not blow up, but it IS NOT TIP4P anymore.
So, careful with analyzing the results!
adrian
On 4/2/13 8:23 AM, Alan wrote:
> Changing dt does solve the problem. Thank you very much.
>
>
> At 2013-04-02 15:30:34,"Gerald Monard" <Gerald.Monard.univ-lorraine.fr> wrote:
>> Hi,
>>
>> From your input file, you use "dt=0.002", which is too large for a
>> non-SHAKE MD. Without SHAKE, you should use dt=0.001 at most (a better
>> set would be dt=0.0005).
>>
>> Gerald.
>>
>> On 04/02/2013 08:12 AM, Alan wrote:
>>> On 04/01/2013 06:08 PM, Gerald Monard wrote:
>>>
>>> Hi,
>>>
>>> As far as I know, TIP4P has been designed as a rigid water model.
>>> However, it should work in AMBER as a flexible model (parameters are
>>> available in frcmod.tip4p). I quickly try a 64 tip4p water system using
>>> either ntc=1 or ntc=2. It works.
>>> What is your input file (mdin)?
>>>
>>> Gerald.
>>>
>>> On 04/01/2013 10:29 AM, Alan wrote:
>>>
>>> Dear all:
>>>
>>>
>>> I'm running an MD of pure tip4p water. The calculation is not very big, so I thought if I could run it without SHAKE. But it turned out I couldn't. Every time I got similar error messages like this:
>>> [cli_0]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> SANDER BOMB in subroutine nonbond_list
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> [cli_3]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>> [cli_4]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
>>> [cli_1]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
>>> [cli_2]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>> list grid memory needs to be reallocated, restart sander
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>> [cli_6]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
>>> list grid memory needs to be reallocated, restart sander
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>> [cli_7]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>> [cli_5]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5
>>> rank 3 in job 1 dell13_38141 caused collective abort of all ranks
>>> exit status of rank 3: return code 1
>>> rank 2 in job 1 dell13_38141 caused collective abort of all ranks
>>> exit status of rank 2: return code 1
>>> rank 1 in job 1 dell13_38141 caused collective abort of all ranks
>>> exit status of rank 1: return code 1
>>> rank 0 in job 1 dell13_38141 caused collective abort of all ranks
>>> exit status of rank 0: return code 1
>>>
>>>
>>> Unit 30 Error on OPEN: density.rst
>>> [cli_0]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> rank 0 in job 1 dell13_32985 caused collective abort of all ranks
>>> exit status of rank 0: killed by signal 9
>>>
>>>
>>> I checked the mailing list but no luck. I've ran similar MD before, the only difference is this time I removed SHAKE. So I added SHAKE back. It worked.
>>> So I'm thinking is SHAKE necessary in running an MD?
>>>
>>>
>>> Thank you.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>>> I tried with heat and density. Without SHAKE, running heat with both sander and sander.MPI will produce a lot of vlimit exceeded for step and finally
>>> SANDER BOMB in subroutine nonbond_list
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>>
>>> running density with sander will produce similar messages. With sander.MPI will produce the message I posted.
>>>
>>> This is the heat.in file that didn't work.
>>> waterbox
>>> &cntrl
>>> imin=0,irest=0,ntx=1,
>>> nstlim=25000,dt=0.002,
>>> cut=8.0, ntb=1,
>>> ntpr=500, ntwx=500,
>>> ntt=3, gamma_ln=2.0,
>>> tempi=0.0, temp0=300.0,
>>> nmropt=1
>>> /
>>> &wt TYPE='TEMP0', istep1=0, istep2=25000,
>>> value1=0.1, value2=300.0, /
>>> &wt TYPE='END' /
>>>
>>> This is the density.in.
>>> density
>>> &cntrl
>>> imin=0,irest=1,ntx=5,
>>> nstlim=25000,dt=0.002,
>>> cut=10.0,ntb=2,ntp=1,taup=1,
>>> ntt=3,gamma_ln=2.0,
>>> temp0=300.0,
>>> ntpr=500,ntwx=500,ntwr=3000,
>>> iwrap=1
>>> /
>>>
>>> When added ntc=2,ntf=2, they will work.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> --
>> ____________________________________________________________________________
>>
>> Prof. Gerald MONARD
>> Theoretical Chemistry and Biochemistry Group
>> SRSMC, Universit¨¦ de Lorraine, CNRS
>> Boulevard des Aiguillettes B.P. 70239
>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>
>> e-mail : Gerald.Monard.univ-lorraine.fr
>> tel. : +33 (0)383.684.381
>> fax : +33 (0)383.684.371
>> web : http://www.monard.info
>>
>> ____________________________________________________________________________
>>
>>
>> _______________________________________________
>> 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
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Apr 02 2013 - 06:00:03 PDT
