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.
>> _______________________________________________
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>> 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
>
>____________________________________________________________________________
>
>
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Received on Tue Apr 02 2013 - 05:30:02 PDT
