[gmx-users] Positioning ions consistently

[Anton Feenstra]

Lieven Buts wrote:
> 
>   I am trying to compare a number of small variations of
> the same protein structure. The protein has a net charge of
> -9 (well, -8.999999, anyway). When I add 9 Na ions to
> the different variations, some of them are put in very
> different positions. This might be an additional source
> of variation between the starting structures.
> 
>   Would it be necessary/useful/pointless to try and
> position the ions more consistently for the different
> structures? Or maybe to leave the ions out altogether?

My suggestion would be to leave them out. I think David also mentioned
this a while ago on the list, the artefacts you can expect from adding 
ions (e.g. insufficient sampling) and from other sources (forcefield, 
limitations of Ewald LR forces) are bigger than from a net charge of 
the system.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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