Nicolas Bock wrote:
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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>
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I suspect that the g96 file is not the right format, plz check it in the
manual. You have named the file something.g96 haven't you?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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