erik.marklund at chem.ox.ac.uk
Thu May 29 11:38:48 CEST 2014
For one ion this would perhaps be possible, but for many ions this becomes a difficult problem. If it's really important I suggest running a simulations where the ions are allowed to equilibrate, possibly with position restraints on any macromolecules you have. It is highly questionable however wether that would make a difference for any subsequent simulation. Na+ will move around your system reasonably quickly anyway.
On 29 May 2014, at 08:04, Atila Petrosian <atila.petrosian at gmail.com> wrote:
> Dear all
> I do not like to replace solvent molecules with Na ions randomly.
> I like to do that based on potential.
> Which option is needed in the end of following line (.....) ?
> genion -s *.tpr -o *.gro -p *.top -pname Na -pq +1 -np 5 .....
> Best wishes
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