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

[Mark Abraham]

David Mobley wrote:
> Mark,
> 
> I've had this same problem anytime I try to use CG to minimize my
> system, so I've always just used L-BFGS or "steep" instead (they work
> fine). I'm not imposing any constraints (constraints= none), but it
> still complains that I can't use CG with constraints, so I haven't the
> foggiest idea what it's complaining about. I can provide mdp, topology
> and .gro files to reproduce this if you'd like. I suspect that either
> (a) the routines for CG consider something *else* a constraint (i.e.
> aside LINCS constraints, etc.), in which case it's possible we have
> that turned on without being aware of it,  or (b) there is a bug in
> the setup for CG.

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