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

[David van der Spoel]

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.
________________________________________________________________________
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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