[gmx-users] genbox error

Justin Lemkul jalemkul at vt.edu
Sun Jan 13 17:45:12 CET 2013

On 1/13/13 11:00 AM, Kieu Thu Nguyen wrote:
> Dear All,
> When i use the command
> genbox -ci single.gro -nmol 175 -box 7.5 7.5 7.5 -try 100 -o 175_noW.gro
> the error is
> Segmentation fault (core dumped)
> What does it mean ?

Google can tell you all about segmentation faults.  You probably ran out of 
memory.  genbox is a memory hog, and when you're trying to insert lots of 
molecules into a box, it gets progressively harder to find space for them.  The 
best solution is to either:

1. Use a larger box and equilibrate to achieve the desired size
2. Insert fewer molecules at a time


> And if i reduce the -try value, the out put file does not contain the right
> number of residues (not 175, and less than).
> Thank for any help !
> Regards,
> KT


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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