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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. -- ------------------------------------------------------ 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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