[gmx-users] grompp with cg does have problem!

[Mark Abraham]

David Mobley wrote:
> Mark,
> 
> It may well be the case that implicit water constraints are the problem, 
> as the follow-up response seems to indicate (I haven't tried it myself). 
> I guess I'd suggest that this be stated explicitly in the manual (and 
> perhaps even in the section on input files which discusses options for 
> minimizers, under the CG section, there should be a note saying that CG 
> won't work with rigid water...).

I filed a Bugzilla report for the same at 
http://bugzilla.gromacs.org/show_bug.cgi?id=37

> Also, perhaps this is naive, but CG works fine in AMBER without doing 
> anything special. It might be worth checking there to see how AMBER 
> handles this. Perhaps it is "properly" handling the water, and if so, 
> GROMACS could do the same thing? Or perhaps it lets the water be 
> flexible? I'm not sure, but it seems like the issue must already be one 
> people have dealt with in these other packages.

It's probably just that constraints aren't implemented in the gromacs CG 
algorithm. It's probably not worth implementing either, given that 
constraints can be used with steepest descent and L-BFGS.

Mark