Amir Marcovitz wrote:
Thank you Justin,
actually, i have two parallel rigid plates that are free to move towards
each other on the Y-axis (i used position restrain on Y and Z axes)
later on i will umbrella sampling to obtain the plate-plate PMF at
various distances from each other (thanks a lot for the helpful tutorial!)
so i will try bond type 6 as you suggested.
up until now i observed , especially during the the NPT run ,that the
atoms are fluctuating , and if the time step was 0.002psec or even 0.001
psec the system was very un-robust and the simulation explodes. (that is
my main concern and the reason for my previous post)
do you think bond type 6 will settle this?
Not likely. If your system is blowing up that means there is something
physically unrealistic about it (insufficient EM or equilibration, inappropriate
parameters or .mdp settings, etc). There's tons of useful information on the
Gromacs site and in the list archive to help you. Otherwise you'll have to
provide substantially more information regarding all the points I raised above
to get any useful advice.
-Justin
anyway, thanks a lot for the quick reply!
Amir
On Thu, Feb 4, 2010 at 7:32 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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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