[gmx-users] Re: mdrun Segmentation fault (after install make_hole_mdrun)

Graham Smith smithgr at cancer.org.uk
Mon Jun 2 17:17:01 CEST 2003

Dear Minghu 

It sounds like you have overwritten your "original" mdrun with the 
hole-making one: you'll have to recompile the standard distribution
again (if you've overwritten the source (.c) files, you'll also 
have to re-unpack the standard source from its tar.gz or rpm 
file). Sorry about that, maybe on reflection I should
have tried to get it to make an executable with a different name. But
I *did* put a file in the distributed mdrun_make_hole.tar.gz
called "README.hole" that tells you: 

1. installation

##### warning! ###### It will replace the existing mdrun and some
source files, so don't extract it into your "main" copy of the
distribution, make a separate copy of the gromacs source distribution
before unpacking it.

The pressure, which I think is calculated from the average over atoms
of f.r (force.postion), will be all wrong during these hole-making
calculations. It should settle down again once you go back to normal
MD (on average:  the value calculated from a single coordinate frame
always tends to have huge fluctuations) 


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