[gmx-users] POPE setup

Marc F. Lensink lensink at bigre.ulb.ac.be
Mon Mar 30 22:08:49 CEST 2009

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


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

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