[gmx-users] create a physiological ion concentration
feenstra at chem.vu.nl
Tue Nov 11 09:54:03 CET 2003
nanyu101 at sina.com wrote:
> Dear gmx-users,
> I want to create a physiological ion concentration for my ion channel+DPPC+water system.I just use genion to replace the water molecule by CA2+ and CL-. After doing this, I have failed to equilibrate the system for the "Fatal error: ci" reason.As my experiences, some atoms crashed. Would you please tell me how to avoid this?
> BTW: before I create the physiological ion concentration, I have put some cations in the right positions of the ion channel and some anions for equilibrium.
> After putting 10 CA2+ and 20 CL- in the ion channel, I have use genion to create a physiological concentration besides the former ions.
> In my system, the concentration of CaCl2 is about 150-200mM and the water molecules in my system is 7000. If I want to create a 200mM concentration, I have to solve 40 CA2+ cations and 80 CL- anions. Because I have already put 10 CA2+ and CL- in the right place of ion channel, there are only 30 CA2+ and 60 CL- remained.
Is that right, IIRC, water is 70M, i.e. 70000 mM.
May that explain your problems, or is the 7000mM a typo?
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users