[gmx-users] genconf

Ur-Rehman, Saif su7 at hw.ac.uk
Wed Aug 10 15:04:03 CEST 2005

I am attempting to run multiple copies of a peptide which I have cut out from beta lactoglobulin. I have been told that the correct way off running multiple copies of a molecules is to utilise the genconf command with the number of copies I wish to use provided as an argument to the n box parameter
Howeever when I run grompp on the outputted conf.gro file  I get this message
processing coordinates...
double-checking input for internal consistency...
ERROR: One of the box vectors is shorter than twice the cut-off length. Increase
 the box size or decrease rlist.
Velocities were taken from a Maxwell distribution at 500 K
There were 4 warnings
Fatal error: There was 1 error
However altering the rllist value in the mdp file or changing the box size has absolutely no effect
Thanking you in advance
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