[gmx-users] bonds section in the topology file

Amir Marcovitz amarcovitz at gmail.com
Thu Feb 4 17:58:02 CET 2010


i'm simulating a surface in water and ions which is composed of 6X6 Carbon
atoms arranged on a 2-d lattice. (using ffamber99)
i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom
(or some other spacing of choice..), and to maintain the surface rigid and

for that i added to the [  bonds ] section at the topology file c0 values
and force constants as following:

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1  3.400000e-01 3.744680e+05
    1     7     1  3.400000e-01 3.744680e+05
    2     3     1  3.400000e-01 3.744680e+05
and so on..

and similarly  added 90 and 180 degrees bond angle constrains between triads
of atoms in the surface according to their location.

the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some
conflict with the definition of C-C bond length which is defined somewhere
in the amber files (if i'm turning the constraint on co off the atoms
approach each other and the spacing is lost)

my questions are:
a) do you think i should define a new dummy atom? and in which files should
it be done? - i'm asking because i didn't find a clear answer in the manual
b) is there any other bond function  (what number?) which may ignore the
definition of the C-C length and treat only the c0 constraint?

if someone can answer or guide me to relevant sections in the manual i'll be
most thankful!
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