[gmx-users] Membrane simulation error

Ben Tam btam125 at hotmail.co.uk
Fri Sep 9 14:49:50 CEST 2016

Dear gromacs user,

I am doing a membrane simulation, however I have this error message pop up when I do energy minimisation:

Program gmx mdrun, VERSION 5.1.1
Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/mdlib/nbnxn_search.c, line: 734

Software inconsistency error:
Lost particles while sorting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I do not understand what the message means. Without the wall, the simulation complete normally and it was ran for 1ns. Can someone enlighten me what is going on and how do I solve the problem?

For the .mdp file, this is my simulation set up for the wall:

nwall= 2
wall_type    = 9-3
wall_r_linpot    = 1
wall_atomtype   = Cw Cw
wall_density    = 5  5
wall_ewald_zfac    = 3

Thank you all for your time to read and help.

Best regards,

Benjamin Tam

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