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

David Mobley dmobley at gmail.com
Fri Dec 16 16:44:22 CET 2005


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...).

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.


> As another poster suggested, perhaps include=-DFLEXIBLE to turn off
> water geometry constraints is what is needed to make CG work. Whether
> the subsequent minimized structure is suitable for starting an MD
> simulation is another question, of course. If normal mode analysis or
> similar is the objective, then this may not be a problem.
> If this is the problem, it's clearly affecting more than one person. How
> can the fact that these implicit water constraints will break CG be made
> more explicit to the user?
> Mark
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