[gmx-users] Format of bond type directives

[Mark Abraham]

Hi

On Sun, Mar 15, 2015 at 9:51 PM, Rajan Kumar <kumarrajan513 at gmail.com>
wrote:

> Hi all,
>
> I am using g_x2top to create topology for my system.
>
> After creating topology file, I see
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     3     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
>     1     4     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
>     1     5     1  1.390000e-01  4.000000e+05  1.390000e-01  4.000000e+05
>     2     3     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
>     2     9     1  1.420000e-01  4.000000e+05  1.420000e-01  4.000000e+05
>
> ------------------------------------------------------------------------------
>
> Please help me understand this format, as the manual explain these
> directive written as something like this:
>
> [ bonds ]
> ; ai    aj    funct      b0        kb
>     1    3    1   0.14310    376560
>     1    2    1   0.14310    376560
>     2    4    1   0.15230    376560


These are the same two columns represented explicitly for the A and B state
(used only if a free-energy perturbation calculation is performed). The
manual example is the normal case. When using FEP, behind the scenes the A
state parameters to the B state unless explicitly stated. It seems g_x2top
writes duplicate data explicitly, and with non-descriptive column headers.
The numbers themselves are in
http://en.wikipedia.org/w/index.php?title=Scientific_notation&section=5#E_notation
.

Mark


> --
> Rajan Kumar
> Indian Institute of Technology, Guwahati
> --
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