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.
-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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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