[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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