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.
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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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Received on Mon Apr 01 2013 - 23:30:02 PDT
