[gmx-users] wrong bonded information in .top/.rtp file produced by g_x2top

[Justin Lemkul]

On 2/28/13 2:45 AM, zhhxu wrote:
> hi all :
>
> I prepared  top and rtp file for graphite using a command:
>
>          g_x2top -f input.gro -r output -o  output in GMX (V 4.5.5).
>
>         A  obvious mistake itp file is posted as below:
> [ bonds ]
>       C1  C3776   1.420e-01   4.000e+05
>       C5  C3780   1.420e-01   4.000e+05
> #####
> for example，the distance between  C1 and C3776 is at least 10 nm.
>   the coordination is below:
> 1GRA       C1    1   0.000   0.000   0.000
> 1GRA    C3776 3776   0.000  10.068   0.000
>
>
> Thanks in advance for any suggestion.
>

The default behavior of g_x2top is to use PBC to measure distances, so if these 
atoms are at opposite "sides" of the box, then they are apparently still within 
bonding distance across the periodic boundary, hence you get a bond.  If this is 
incorrect, then either use a larger box or use -nopbc.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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