[gmx-users] do the non-bong ennergy influence the opt imization?

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 25 09:14:17 CEST 2006

zzhwise1 wrote:
> hi all
>     as i use the l-bfgs to optimize my system ,which composed of two 
> monolayers that each contain 36 CH3(CH2)14COOH molecules ,when the 
> distance bettwen the two monolayes is 1.5nm,the minimization go 
> smoothly,but when  decrease to 1.2nm,the monilayers turn over(A-B:B-A TO 
> B-A:A-B,A B are  the tail groups),but when i increase the molecules from 
> 36 to 108,the monolayers also turn over at 1.5nm.and the mdp is
> rlist               =  0.9
> rcoulomb            =  0.9
> vdwtype             = shift
> rvdw-switch         = 0.7
> rvdw                = 0.8
> do the non-bond cause the problem? 
You definitely want a longer cut-off for the Van der Waals, e.g.
rvdw_switch = 0.9
rvdw           = 1.1
rlist = 1.1
rcoulomb = 1.1
coulomb_type = pme

further you could increase the box size perpendicular to the interfaces.
Is there water between the monolayers?
I suspect that what you call "turning over" really is not a real, but it
looks like that due to periodic boundary conditions (hence the
suggestion to increase the box size). In an energy minimization no large
conformational changes occur.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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