[gmx-users] Adding Na ions to DPPG

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 15:07:48 CET 2008

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 ]
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.


>> 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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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