[gmx-users] .gro files problems

Andrew Voronkov drugdesign at yandex.ru
Fri Mar 6 19:06:21 CET 2009

Dear GROMACS users,
I'm trying to do this tutorial

with 1ijy structure from rcsb.org
All .gro files on different step raise questions.
1) conf.gro - by VMD I see some strange groups which are not linked with the protein.
2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this?
3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems...

The .gro files are in the attachment.
On minimization step I also get:
Steepest Descents converged to machine precision in 73 steps,
but did not reach the requested Fmax
On equilibration step I also get an error(with such .gro file it very proabable):

Warning: 1-4 interaction between 2 and 19 at distance 2.795 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.000 ps: Water molecule starting at atom 33175 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault

Best regards,

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