[gmx-users] grompp with cg does have problem!
Mark.Abraham at anu.edu.au
Thu Dec 15 22:30:53 CET 2005
David Mobley wrote:
> 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?
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