[gmx-users] table extension problem

Fernando Mattio mattiofer at gmail.com
Thu Nov 24 15:36:18 CET 2005

   Hi Berk,
   I think  I understood what you  wrote.... But... Why the  simulation
with  just part of the  ice  runned until the end??? Maybe  because  the
size of the ice wasn´t very significant??? So maybe if I just increase my
box size it perhaps works... What´s your opinion about?
   Anyway, if it didn´t work, then I must not use pressure coupling, and for
this reason I will have no control about the pressure, is it right?

  Thanks again
  Fernando Mattio

2005/11/24, Berk Hess <gmx3 at hotmail.com>:
> >From: Fernando Mattio <mattiofer at gmail.com>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: [gmx-users] table extension problem
> >Date: Thu, 24 Nov 2005 14:46:19 +0100
> >
> >Dear Gromacs users,
> >
> >When I tried to run my simulation (that consists of a box with 55969 mol
> of
> >solvent,  one protein and  1860  water molecules to be treated as ice so
> I
> >applied the frozen group option to keep it´s  original
> coordenations)  with
> >just 26 of my "ice molecules"  everything went ok, but when I tried to
> run
> >with all of them I got fatal errors related to table extension, so it
> >crashed always on step 2.
> You can't freeze all the water and use pressure coupling.
> All the waters are fixed in space, while the box size is scaled,
> this causes the problems.
> A solution would be to also scale the frozen coordinates,
> but this has not (yet) been implemented in Gromacs.
> Berk.
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