[gmx-users] MD of crystal

[David van der Spoel]

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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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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