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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