[gmx-users] Re: mdrun_hole

[Graham Smith]

Pedro Alexandre Lapido Loureiro wrote: 

> when I try to run mdrun_hole, the program halts due to LINCS
> violation in the water molecules of my DPPC/water/protein system. 

> Here is my hp.mdp file:

looks fine to me. 

> Is this a common problem?  Obviously, I can begin my insertion
> process with the water already in place, can't I? 

Yes, you can. 
When you say "DPPC/water/protein system", you of course haven't got
the *protein* present when you're trying to make the hole, have you?

What happens if you try to run the tpr file with 'normal' mdrun 
and no hole stuff? Is it OK? (at least for a bit; the hole you made
with the perl script might make it crash in the end I suppose). 

Somebody told me recently that they'd had trouble with nose-hoover T
coupling and parinello-rahman P coupling with mdrun-hole; it would be
better to use berendsen. That doesn't sound like the source of your
problem though.

G 

########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr