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Hello list,<BR>
<BR>
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:<BR>
<BR>
2<BR>
bcc Na<BR>
Na 0 0 0<BR>
Na 0.2145 0.2145 0.2145<BR>
<BR>
Then I ran babel on it and created a gromos96 file:<BR>
<BR>
#GENERATED BY OPEN BABEL 2.0.2<BR>
TITLE<BR>
bcc Na<BR>
END<BR>
POSITION<BR>
0 LIG NA 1 0.00000 0.00000 0.00000<BR>
0 LIG NA 2 0.21450 0.21450 0.21450<BR>
END<BR>
<BR>
Then I figured I use genconf to multiply this cell and put together a larger supercell with this bcc structure. I ran<BR>
<BR>
genconf -nbox 5 5 5<BR>
<BR>
but I got this error message:<BR>
<BR>
-------------------------------------------------------<BR>
Program genconf, VERSION 3.3.1<BR>
Source code file: smalloc.c, line: 113<BR>
<BR>
Fatal error:<BR>
calloc for atoms->atomname (nelem=-1753458140, elsize=4, file typedefs.c, line 237)<BR>
-------------------------------------------------------<BR>
<BR>
I have no idea what's going on here. Could someone give me a hand?<BR>
<BR>
Thanks, nick<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
On Wed, 2007-02-14 at 22:04 +0100, carl caleman wrote:
<BLOCKQUOTE TYPE=CITE>
<PRE>
<FONT COLOR="#000000">Hi</FONT>
<FONT COLOR="#000000">My suggestion is that you run the tutorial, that will give you an idea </FONT>
<FONT COLOR="#000000">how it all works. Then you can modify the files used in the tutorial and </FONT>
<FONT COLOR="#000000">run you simmulations. If you never done it before it will take you some </FONT>
<FONT COLOR="#000000">time to get it started but you can do it.</FONT>
<FONT COLOR="#000000">/Calle</FONT>
<FONT COLOR="#000000">Nicolas Bock wrote:</FONT>
<FONT COLOR="#000000">> Hello list,</FONT>
<FONT COLOR="#000000">></FONT>
<FONT COLOR="#000000">> I would like to run an MD simulation to simulate the melting of a </FONT>
<FONT COLOR="#000000">> metallic crystal. Can this be relatively simply done in GROMACS? I </FONT>
<FONT COLOR="#000000">> have the pair potential between the ions and ion configurations I </FONT>
<FONT COLOR="#000000">> would like to start with. I tried to work my way through the GROMACS </FONT>
<FONT COLOR="#000000">> manual but I am having a hard time understanding how to set something </FONT>
<FONT COLOR="#000000">> like this up. Could someone point me in the right direction, please?</FONT>
<FONT COLOR="#000000">></FONT>
<FONT COLOR="#000000">> Thanks, nick</FONT>
<FONT COLOR="#000000">></FONT>
<FONT COLOR="#000000">> ------------------------------------------------------------------------</FONT>
<FONT COLOR="#000000">></FONT>
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</PRE>
</BLOCKQUOTE>
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