[gmx-users] wrong bonded information in .top/.rtp file produced by g_x2top
jalemkul at vt.edu
Thu Feb 28 14:52:37 CET 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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