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, Université 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 - 01:00:03 PDT
