[gmx-users] Adding Na ions to DPPG

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 15:18:10 CET 2008

On Monday 27 October 2008 15:07, Justin A. Lemkul wrote:
> Peyman Yamin wrote:
> > On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
> >
> > Actually I'm doing a funny mistake telling I should replace an O with an
> > Na! (probably because of high adrenaline level in my blood for the
> > deadline is near!) I should just put one Na beside the O I have! I simply
> > have a PO4 where one O has no H and thus is negative. an Na+ should
> > accompany this O.
> Well that makes more sense.  I'm assuming you have a DPPG bilayer with
> solvent? Or are you simulating a single DPPG in vacuo?  If it's a bilayer
> in solution, just use genion; you can even specify exactly how many Na+ you
> want using -np.
> If the topology organization is confusing you, refer to Chapter 5 of the
> manual. If you make a .top for DPPG, you can specify:
> [ molecules ]
> DPPG	x
> NA+	1 (or whatever)
> after including the appropriate force field call and ions.itp; the
> parameters for all atom types are taken from these files.

Well this looks great! 
I simulate one single DPPG in solvent. and you know, this Na+ is not in 
solvent but a part of DPPG. So you mean I just make a DPPG with an O which 
has no H so is minus and then use genion to add Na? will it place the Na 
aroung O hopefully? I think if I put no H arounf O the prodrg will force me 
to have it! so I should delete it and replace it with Na? or I should never 
use the word "replace" at all???

Thanks again ;)

> -Justin
> >> 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. 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:
> >>
> >> Are you trying to replace the O in DPPG with Na+?  Or are you simply
> >> trying to add ions to the surrounding solvent (water)?  If you just need
> >> ions in the solvent, use genion; you don't have to do it manually.
> >>
> >>> * 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 ?
> >>
> >> Again, I'm not clear on what you're trying to accomplish.  If you
> >> replace one of these oxygen atoms, you will likely not have an integer
> >> charge within the DPPG molecule itself.
> >>
> >>> * 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?
> >>
> >> Simply #include "ffG43a1.itp" at the top of your .top file; it will
> >> include nonbonded and bonded parameters for all the atoms in the system.
> >>
> >> -Justin
> >>
> >>> Thanks in advance for the time,
> >>> I've been away for some time from GMX and might sound
> >>>
> >>> Cheers,
> >>> Peyman

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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