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

[Mark Abraham]

Manik Mayur wrote:
> 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.

So, what algorithm are you using for your long-ranged electrostatic 
interactions? Do you know roughly how it works? Does it then make sense 
to try to exclude some of the long-range interactions?

> 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?)

You have atoms that are not part of a charge group (or, probably, are 
part of one of size one and charge zero.

> 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-

No, that's the dump from MPI after the error. You need to consult both 
the stdout and the .log file.

Mark

> 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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