[gmx-users] something wrong about making hole

Erik Lindahl lindahl at stanford.edu
Fri Feb 21 03:57:05 CET 2003

HI Xianhui,

> Back Off! I just backed up insert.trr to ./#insert.trr.2#
> step 120, will finish at Thu Feb 20 19:04:24 2003Wrote pdb files with 
> previous and current coordinates
> Warning: 1-4 interaction at distance larger than 2.25
> These are ignored for the rest of the simulation
> turn on -debug for more information
> Fatal error: ci = -2147483648 should be in 0 .. 2534 [FILE nsgrid.c, 
> LINE 210]
This error message is described in the FAQ, both in the distribution 
files and on the website.

In general, making holes and inserting proteins in lipid bilayers is a 
complicated procedure, and it is even more difficult to do it without 
destroying the structure of the protein. Just as in experimental 
science, you have to examine and understand the methods you are using; 
you cannot just apply brute force and press a button.

In this case it is quite obvious that something is wrong with your 
coordinates - atoms are clashing into each other or something. Start by 
reading the available documentation, and then locate the problem in 
your system.

The best idea for you might be to start with a couple of simple 
membrane systems, and once you've figured out how to use different 
minimization and molecular dynamics techniques you can move on to more 
complex systems like proteins in membranes!



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