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 ;) 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
