[gmx-users] Re: Simulation problem with extended membrane system!

[chris.neale at utoronto.ca]

If you use the script as I have suggested,
http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html

The script is designed for a gro file that does not have any  
velocities written into it, ie. it looks like this:

     1THR      N    1   0.801   6.473  -0.310
     1THR     H1    2   0.760   6.476  -0.402
     1THR     H2    3   0.865   6.394  -0.304

If you have 3 additional columns in your .gro file, then you need to  
change the script like this:

   l=${#line}
   m=$(expr $l - 24)  # ADD THIS LINE ONLY IF VELOCITIES ARE IN YOUR .GRO

The first line is #37 I think, and the next line is the line that you  
need to add. This says "Ignore the velocities"

Also, if you use TIP4p then line 30 needs to be
   if [ "$count" = 4 ]; then
instead of
   if [ "$count" = 3 ]; then

Likewise, use "5" if you use tip5p.

Chris.