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
option.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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