[gmx-users] POPE setup

[Marc F. Lensink]

On Mon, Mar 30, 2009 at 06:43:37AM -0600, Peter Tieleman wrote:
> Hi,
> 
> I noticed several comments on problems with POPE in vacuum. I haven't 
> made POPE systems in quite a while, but perhaps it would be an idea to 
> temporarily set the charge of the H-atoms on the NH3+ group to zero, or 
> add exclusions between the H atoms and the phosphate oxygens. I haven't 
> tried this with inflategro but setting the charges to 0 did help with 
> manipulating POPE lipids when I worked on OmpF. Just don't forget to 
> revert to the original itp file for real work.

I can confirm that.  I've used inflategro recently with POPE.  in one
case no problems, in another I indeed solved it by decreasing the
charges.

cheers,
marc




-- 
Marc F. Lensink (Ph.D.)
Structure and Function of Biological Membranes            SFMB
Centre for Structural Biology and Bioinformatics          CSBB
Université Libre de Bruxelles (ULB)     marc.lensink at ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425