[gmx-users] .gro files problems

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 6 19:41:28 CET 2009

Andrew Voronkov wrote:
> Dear GROMACS users,
> I'm trying to do this tutorial

It's always best to post a link to the tutorial you're using.  There are dozens 
of Gromacs tutorials out there.

> 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.

This may or may not be an artefact of VMD's efforts to guess where bonds should 
be.  Sometimes it's smart, sometimes it's not.

> 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?

editconf -c

> 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...

Use editconf -c and try again.

> The .gro files are in the attachment.

The listserv ate them, but they probably won't aid much in diagnosis, anyway.

> On minimization step I also get:
> Steepest Descents converged to machine precision in 73 steps,
> but did not reach the requested Fmax

Depending on what your target Fmax was, this may not be a problem.  Fmax < 1000 
is generally adequate for a simple protein in water.

> On equilibration step I also get an error(with such .gro file it very proabable):

Or you could have an error in your .mdp file (inappropriate parameters, etc), so 
if things continue to fail, post the .mdp file (not as an attachment, just embed 
the text).


> 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,
> Andrew
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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