[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top
Jose Borreguero
borreguero at gmail.com
Wed Jun 21 16:47:46 CEST 2017
Dear Gromacs users,
I created the .top file for a small silica crystal that contains only two
types of atoms, silicon (type SIO) and oxygen (type OSI). The bond
potential is:
[ bondtypes ]
; i j func b0 kb
SIO OSI 1
0.15783
251040
After running gmx x2top, the .top file contains
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 9 1 1.600000e-01 4.000000e+05 1.600000e-01 4.000000e+05
1 35 1 1.600000e-01 4.000000e+05 1.600000e-01 4.000000e+05
I
assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I
was expecting number 251040 for c1 and c3, got
400000 instead
!
I don't know the meaning of coefficients c0, c1, c2, and c3
,
I could not find some explanation for them
.
Can anyone point to a place where these coefficients are described in
detail? The description may explain the
400000
number.
Best,
.Jose
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