[gmx-users] grompp error testing water

[Erik Lindahl]

Hi Bjorn,

>
> 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.
>

Hm, it works perfectly for me. In what directory are you running, and 
exactly what command are you issuing?

The problem might be caused by including a file twice, but I'm not sure 
why that would happen...

If you still haven't found it, try running grompp with the -pp option 
to write out the preprocessed file, and check if there are multiple 
atomtype or nonbonded sections in that file.

Cheers,

Erik