[gmx-users] bonds section in the topology file

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 4 18:32:08 CET 2010

Amir Marcovitz wrote:
> Hi,
> 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 planar
> 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?

Two options I can think of:

1. Why not position restrain your carbon lattices to parallel planes?
2. Use bond type 6 to define a harmonic potential between the atoms you want to 
restrain.  If the two lattices are part of the same molecultype definition 
(unclear from your post), then you can use distance restraints.  If they are 
separate molecules, however, you can't, and hence why bond type 6 is a viable 


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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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