[gmx-users] grompp error testing water

[Bjorn Sveinbjoronsson]

Erik,

Thank you for the help so far. I'm confused as to whether I should send my e-
mails into the mailing list or some other form. On response to my e-mail on 
Feb. 19, you said, "The list only accepts e-mail from subsribers to protect 
from spam."  I had tried signing up for the list and was starting to get e-
mails.  I realize up must get alot of e-mails related to Gromacs every day and 
that it is not your full-time job (or at least would like it not to be).  So, 
please set me straight.  

I have now completed the installation process. The gmxdemo appears to work 
fine, other than the ngmx command not being recognized. (I don't have motif or 
lesstif installed).  However, I am running into problems when I run the grompp 
process for the water example. It appears that the LJ-14 values in the 
ffgmxnb.itp file are different than in another file.  I am not sure which file 
this would be.  I increase the number of allowable warnings to 1000 and it 
became apparant that there where other files from this folder which were also 
not the same as the 'default' files.

The text is as follows:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "/home/Administrator/gromacs-3.1.4/share/top/ffgmxnb.itp". line 
272]:
   Overrinding LJ-14 parameters,
   old:0.0022617 7.4158E-07 0 0
   new: O OW 1 0.24329E-02 0.74158E-06

WARNING 2
.
.
.
etc.....

Thank you again for all the help.

Cheers,
Bjorn