[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Justin Lemkul]

On 6/21/17 10:47 AM, Jose Borreguero wrote:
> 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.
> ​

It's the default bonded force constant.

gmx help x2top
"
...
  -kb    <real>   (400000)   Bonded force constant (kJ/mol/nm^2)
...
"

The comment line means little, so there's no specific meaning to c0, c1, etc. 
It generically refers to bonded parameter fields, which for bonds are A- and 
B-state equilibrium lengths and force constants.  For dihedrals these mean 
something entirely different.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================