[gmx-users] warning for overwritten dihedrals

[Erik Lindahl]

David L. Bostick wrote:
> I just installed gmx-3.1.3 and ran grompp on a system that had previously
> worked with gmx3.1 , but this time got several warnings for overwritten
> dihedral potentials like this..
> 
> WARNING 4 [file gromppdWolUa, line 4853]:
>   Overriding Proper Dih. parameters,
>   old: 0 1.046 3 0 0 0
>   new: P   OA    1     0.000       3.138      2
>  
> WARNING 5 [file gromppdWolUa, line 4856]:
>   Overriding Proper Dih. parameters,
>   old: 0 1.046 3 0 0 0
>   new: OS    P    1     0.000       3.138      2
> 
> If grompp is okay, then I would like to check to see where my topology and
> the one grompp expects to recieve differ.  Given the form of the warning, I
> am not sure how to begin searching my topology for the dihedrals that have
> been changed.  I don't understand the format of the numbers given
> after the "old:" in the warning, but the ones after "new:" look readable,
> 

Hi David,

For various reasons grompp uses a 'stack' where we push types and bonds.
A later line will overwrite previous parameters, but you get the type of 
warning you see.

The previous parameters probably include the B state, which are implied 
to be 0 when you not include them. Check for previous dihedral lines 
with P-OA or OA-P!

The CVS version supports dihedraltypes defined with either 2 or 4 atoms, 
by the way.


> I may wish to keep these changed parameters.  What do I do then?  If grompp
> gives me too many warnings (more than 10 I think) it will cut out.  How do
> I force it to write a .tpr file anyway?
> 

Just give a large number in the '-maxwarn' option. The reason for 
aborting is just to stop users who don't read/care about the warnings...

Cheers,

Erik