Hello everyone,
I have a topology and coordinate files I have being using to run some simulations on Gromacs. I have converted them to Amber format using gromber and did a visual inspection on VMD to check everything looks fine.
Then, to do a simple test I ran am energy minimization (in vacuum) just to check if there was anything wrong with the converted topology and/or coordinate files that was not noticed during the visual inspection.
If I ran the serial version of Sander, the minimization finishes with no error or warning messages. However, if I ran the MPI version on 32 processors I get the following message and the calculation is aborted:
* NB pairs 336 304647 exceeds capacity ( 304964) 17
SIZE OF NONBOND LIST = 304964
SANDER BOMB in subroutine nonbond_list
Non bond list overflow!
check MAXPR in locmem.F90
If I reduce the number of processors to 16, I get different messages:
***** Processor 7
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1800 Allocated: 533
***** Processor 8
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 3000 Allocated: 533
***** Processor 9
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1201 Allocated: 533
However, the calculation finishes and the final structure is the same as the one acquired with the serial version that does not display any of these messages.
My system is a crystal slab of CaCO3 with an additional Ca ion on top of it, with maximum z coordinate being ~ 14 angstrons. The box parameters are a=64.8200000 b=64.8199633 c=100.0000000 alpha=90.0000000 beta=90.0000000 gamma=101.9300396.
For reference, my mdin file is:
test energy minimization
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 1,
igb = 0,
cut = 12
/
The message about the exceeding number of non-bond interactions would suggest something wrong with my system, but the serial version does not complain about anything. Reducing the number of processors changes the message displayed (not complaining about exceeding number of non-bond interactions anymore) and it seems to run fine, because the final structure is the same as the one acquired with the serial version.
Can someone help me understanding what may be going on? I can provide my input files, if necessary.
Best regards,
Felipe
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Received on Wed Jun 25 2025 - 12:00:02 PDT
