[gmx-users] Re: mdrun_hole

[Pedro Alexandre Lapido Loureiro]

Citando Graham Smith <smithgr at cancer.org.uk>:

> 
> 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 
> 
Thanks for your reply and sorry: it was my mistake!
My topology file was in a "shuffled" configuration:
..
DPPC
SOL
DPPC
SOL
..
(the input .gro file was "unshuffled").
Somehow it caused that error.
Cheers,

Pedro.
--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil