Hello list,
I need your help. I started playing around and began to set up my
crystal. I am having some issues though. I don't know whether that's
because something is wrong with my installation or with my inputs. Here
is what I did: I generated an xyz file with a 2 atom Na atom
configuration. I put the Na in a bcc structure:
2
bcc Na
Na 0 0 0
Na 0.2145 0.2145 0.2145
Then I ran babel on it and created a gromos96 file:
#GENERATED BY OPEN BABEL 2.0.2
TITLE
bcc Na
END
POSITION
0 LIG NA 1 0.00000 0.00000 0.00000
0 LIG NA 2 0.21450 0.21450 0.21450
END
Then I figured I use genconf to multiply this cell and put together a
larger supercell with this bcc structure. I ran
genconf -nbox 5 5 5
but I got this error message:
-------------------------------------------------------
Program genconf, VERSION 3.3.1
Source code file: smalloc.c, line: 113
Fatal error:
calloc for atoms->atomname (nelem=-1753458140, elsize=4, file
typedefs.c, line 237)
-------------------------------------------------------
I have no idea what's going on here. Could someone give me a hand?
Thanks, nick
On Wed, 2007-02-14 at 22:04 +0100, carl caleman wrote:
> Hi
>
> My suggestion is that you run the tutorial, that will give you an idea
> how it all works. Then you can modify the files used in the tutorial and
> run you simmulations. If you never done it before it will take you some
> time to get it started but you can do it.
>
> /Calle
>
> Nicolas Bock wrote:
> > Hello list,
> >
> > I would like to run an MD simulation to simulate the melting of a
> > metallic crystal. Can this be relatively simply done in GROMACS? I
> > have the pair potential between the ions and ion configurations I
> > would like to start with. I tried to work my way through the GROMACS
> > manual but I am having a hard time understanding how to set something
> > like this up. Could someone point me in the right direction, please?
> >
> > Thanks, nick
> >
> > ------------------------------------------------------------------------
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