RE: [gmx-users] counterions?

[Samuel C Flores]

Hmm..   Well counting the charged residues leads to scores of ions, which I think would be a tight squeeze in my water box, given that each ion should have a hydration shell around it.     I like the idea of neutralizing, then adding ions to reach a certain ionic strength.  However how to know exactly what ionic strength I need?  I am modeling murA, but haven’t found an ionic strength in the literature.  Also, wouldn’t the ionic strength near the protein be different from that elsewhere in the solution?       Sam   From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ran Friedman Sent: Sunday, July 16, 2006 12:57 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] counterions?   Hi, If you want to add ions near charged residues and want to know how much, just count the number of charged residues, and add one positive and one negative charge for the N- and C- termini. You can use g_sas to locate the solvent-exposed residues if that's needed.  However, I think that no matter where you put the ions, they will relocate once the simulation equilibrates. So it may be better just to put enough ions to neutralise the system. You can then add some ions to reach the desired ionic strength. genion can be used to randomly put the ions in place, which makes sense since they're very mobile anyhow. Hope that helps, Ran. Samuel C Flores wrote:     Hi Guys,     Can anyone tell me how I should go about adding counterions in GROMACS? Right now I am adding just enough counterions to make the net charge equal to zero.  However I believe I should be adding a counterion for each charged atom on the surface, according to some algorithm.  Is there some program out there, similar to Amber's CION, for deciding how many counterions to supply? I think I can use genion to actually place them, right now I just want to know how many I need..     Sam       +++++++++++++++++++++++++++++++++++++++++++ This Mail Was Scanned By Mail-seCure System at the Tel-Aviv University CC.     _______________________________________________ gmx-users mailing list    gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- ------------------------------------------------------ Ran Friedman http://bioinfo.tau.ac.il/~ran Laser Laboratory for Fast Reactions in Biology Department of Biochemistry Faculty of Life Sciences Tel-Aviv University Tel. +972-3-6409824 Fax. +972-3-6409875 ------------------------------------------------------

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