[gmx-users] Adding Na ions to DPPG

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 15:21:55 CET 2008

Peyman Yamin wrote:
> 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???

Well, the Na+ may be associated with DPPG electrostatically, but they are still 
distinct chemical entities.  You can have a DPPG that has a net -1 charge; 
certainly all chemical species are not net neutral!  Indeed, genion will place 
Na+ in whatever solvent you choose, but may not necessarily be bound to DPPG. 
Some simulation may show the association, however.

And no, don't replace any part of your DPPG.  Because then you don't really have 
DPPG any more do you?


> Thanks again ;)
> Peyman
>> -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


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


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