[gmx-users] Adding Na ions to DPPG

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 13:35:47 CET 2008

Dear GMX users,

I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure 
with the Na replaced with O. 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? 

Thanks in advance for the time,
I've been away for some time from GMX and might sound 


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

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