[gmx-users] create a physiological ion concentration

David spoel at xray.bmc.uu.se
Tue Nov 11 08:31:01 CET 2003

On Tue, 2003-11-11 at 03:34, 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.
> genion -s ion_channel.tpr -np 30 -pname CA2+ -pq 2 -nn 60 -nname CL- -nq -1 -n ion_channel.ndx -o ion_channel.pdb
> But I have failed in equilibrating the ion_channel.pdb. Would you please give me some advices? Any comment is appreciated.

try using the random option for genion, and start your simulation with
position restraints on lipids, protein and the ions in the channel (and
constant volume too). After that release the volume (ie NPT) then
release the lipids and finally protein and ions. You wil have to do a
couple of equilibration steps before you can run the production

> Best wishes,
> nanyu
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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