[gmx-users] dppc simulation

Michael Patra patra at lorentz.leidenuniv.nl
Sun Nov 7 19:34:08 CET 2004


I didn't experience any problems when I did my simulations of methanol
and water with a DPPC membrane, see http://www.arxiv.org/abs/cond-mat/0408122.
Please check with "trjconv -pbc inbox" whether you actually are having
a problem, or whether you just got confused by the sometime counter-
intuitive results caused by Gromacs' way of assigning lipid molecules
to the simulation box or its mirror image.


- Michael Patra
> Dear gromacs users,
>         I am trying to simulate a system in which I had mixture of methanol
> and water on either side of DPPC bilayer.I performed energyminimization and
> then when I was trying to simulate the system I was gettimg ridiculous
> result,a monolayer came closer to the other and then all the water and
> methanol molecules spread away in the simulation box and then monolayer got
> splitted into two halfs and what not,it was ridiculous to explain too,could
> anyone guess where the major mistake might have beeen,I have used the same
> input parameter file which I have used earlier for simulating water on
> either side of the dppc bilayer.
>   Any suggestion would be greatly appreciated........
> Thanking you,
> Dinesh.
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