[gmx-users] MD of crystal

[Nicolas Bock]

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
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070215/2e6bb730/attachment.html>