[gmx-users] Adding Na ions to DPPG

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 14:58:52 CET 2008

On Monday 27 October 2008 14:08, Mark Abraham wrote:
> Peyman Yamin wrote:
> > Dear GMX users,
> >
> > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the
> > structure with the Na replaced with O.
> That doesn't make sense to me.
> > I get a .top with this from prodrg and try to
> > add the Na manually at the right place by removing the corresponding O. I
> > use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem:
> >
> >
> > * In .top file, as far as I can understand, I should just replace OA with
> > NA+ and set the mass and charge.
> > DPPG has a centre:  [ O-P(O)=O ] -
> > The Na+ should be around this with +1 charge.
> > should I put charge +1 ?
> >
> > * which parameters should I place in the top as the Na+ is not bonding. I
> > need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp.
> > (NA+ OA) but I'm not sure where should I put it in the top file. What
> > should I insert manually in top file at all?
> Sodium is not going to form any bond. It's a labile ion, so needs its
> own [ molecule ] section. The easiest approach is to construct a
> topology for the anion, and then use genion to add suitable amounts of
> Na+ afterwards. Check out some tutorial material for the approach here.

Right, but can't I have them all included in a single top??
What shall I put into the topology of the cation then? I have a single DPPG 
molecule in water/octanol. So I thought I might just embed the Na inside the 
DPPG top. in the end DPPG HAS a Na actually, though non-bonded!

If I'm way away from making sense then would be happy to know the logical way. 
about genion I thought it's mainly for adding the ions to the solvent, but I 
should have exactly one Na. 

Be well,

> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

More information about the gromacs.org_gmx-users mailing list