[gmx-users] Re: solvation

[Jamie Seyed]

Hi all,
Thanks for your comments. Actually as Vitaly mentioned I am still try to
visualize the gro-file made by genbox. I found out for any number that I use
for "-nmol ? -ci insert.gro" after some iterations and upto these values:
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
I get segmentation fault. In fact cut-off values from 0.1 in the case of
-nmol 0, jumps to 0.45 in the case of -nmol 1 and then it gives me
segmentation fault. The only way to get rid of it is put -nmol 0!
Now my questions are:
(1) What can be wrong in my insert.gro file. Does it matter the coordinates
of 1 molecule that I obtained from spc216.gro file?? The format is the same.
(2) This command will try to add water where? In the same coordinates as
insert.gro??
What is your suggestions?? Many Thanks in Advance/Jamie

On Thu, Aug 13, 2009 at 5:25 PM, Vitaly V. Chaban <vvchaban at gmail.com>wrote:

> Tsjerk,
>
> I understood the situation in such a way that MD was not run at all,
> so Jamie visualizes *gro* file obtained with *genbox*...
>
> Jamie,
> didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/
> to prepare your system?
>
>
> Vitaly
>
>
> >
> >> Thanks for the answer. When I said far away means my pore was in one
> corner
> >> of vmd window and the water molecules in opposite corner (almost).
> >
> > Did I miss something or did neither Vitaly nor Justin reply "Are you
> > perhaps seeing the effect of periodic boundary conditions?".
> >
> > Tsjerk
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
>
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