2016-05-04 8:07 GMT-06:00 Chang Woon Jang <[email protected]>:
> Dear Votca Users,
>
> I have very simple question. I have two molecules in a system. The first
> molecule consists of five beads (A-B-C-B-A) and three bead types, and the
> second molecule has three beads (D-E-D) and two bead types. Thus, I have
> three bond and angle potentials, table_b1.xvg, table_b2.xvg, table_b3.xvg,
> table_a1.xvg, table_a2.xvg, and table_a3.xvg.
>
> table_b1.xvg : A-B
> table_b2.xvg : B-C
> table_b3.xvg : D-E
> table_a1.xvg : A-B-C
> table_a2.xvg : B-C-B
> table_a3.xvg : D-E-D
>
>
> I ran IBI to obtain non-bonded potentials. How do IBI calculation figure out
> which tabulated potentials matching which bond and angle? Should the
> topology file configure the potentials?
In the gromacs' topol.top, each molecule has a bonds and angle block, e.g.
[ bonds ]
1 2 8 1 1.0
2 3 8 1 1.0
[ angles ]
1 2 3 8 1 1.0
The "8" in column 3 (for bonds) and 4 (for angles) means use a
tabulated potential. The "1" in column 4 (and 5 for angles) is the
table number, i.e. the number in filename e.g. table_b1.xvg
See Section 4.2.14 of the gromacs manual
(ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf) for details.
Christoph
>
> Thank you.
>
> Best regards,
> Changwoon Jang,
>
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--
Christoph Junghans
Web: http://www.compphys.de
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