[gmx-users] Re: Issues regarding exclusions and Charge group distribution

[Manik Mayur]

Hi,

The last mail supposedly bounced from the server due to attachments. So
please excuse in case you find this as a repetition.

I am trying to simulate a system where I want to exclude all nb interactions
between frozen groups. So I followed the manual and defined them in
energygrp_excl. But upon doing that it throws the following warning.

WARNING 1 [file topol.top, line 1583]:
  Can not exclude the lattice Coulomb energy between energy groups

What is the reason of the warning and should I be worried about it or safely
ignore it.

Next, I am facing a strange problem with mdrun_mpi. If I run it on 4 nodes
then it throws up the following error. Which I traced to md.log where I saw:

There are: 15923 Atoms
Charge group distribution at step 0: 0 3264 3185 0 (why these zeroes?)
Grid: 3 x 4 x 5 cells

However with 2 nodes it has and runs fine:

There are: 15923 Atoms
Charge group distribution at step 0: 3226 3223
Grid: 4 x 5 x 25 cells

The error-

Making 1D domain decomposition 1 x 1 x 4
starting mdrun 'TransverseElectrode'
100000 steps,    200.0 ps.
step 0

NOTE: Turning on dynamic load balancing

[md-comp1:32374] *** Process received signal ***
[md-comp1:32377] *** Process received signal ***
[md-comp1:32377] Signal: Segmentation fault (11)
[md-comp1:32377] Signal code: Address not mapped (1)
[md-comp1:32377] Failing at address: (nil)
[md-comp1:32374] Signal: Segmentation fault (11)
[md-comp1:32374] Signal code: Address not mapped (1)
[md-comp1:32374] Failing at address: (nil)
[md-comp1:32377] [ 0] [0xb7fd8440]
[md-comp1:32374] [ 0] [0xb7ef0440]
[md-comp1:32374] *** End of error message ***
[md-comp1:32377] *** End of error message ***

I would be extremely thankful, if somebody points me to the source of the
error and the workaround.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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