[gmx-users] Repulsion instead of adsorption

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 15 21:43:46 CET 2011

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.


> any help will highly appreciated.


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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