mina Madah wrote:
Dear all
I'm working on simulation of adsorption on the sheet .
I use periodic boundary conditions in two dimension (X,Y) .
in my work the initial configurations were minimized at first then
system equilibrated for 100 ps and followed by 500 ps production run.
when I look at the .xtc and .gro file by " vmd " in the end of my work
(after final mdrun), the particles are so much far from the sheet and
realy no adsorption occur.sheet repulsed particles I also understood
that after equilibration step the particle start to geting distance from
sheet.
I made the parameters of force field for the sheet by own ( bonding and
nonbonding ) , because a proper force field for my compound didn't
exist in defualt gromacs.
why adsorption don't occur ?
Either your model (parameters, initial configuration, etc) is wrong or you
didn't simulate long enough. 500 ps is an extremely short timeframe.
-Justin
any help will highly appreciated.
--
========================================
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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