[gmx-users] genion-Cl

X.Periole X.Periole at rug.nl
Thu Mar 3 08:28:39 CET 2005

>> After ideally generated the Cl- location with the
>>"genion -random...", i started to run energy minimization
>>by 200 steps "sd". I noticed the Cl- move to the protein
>>after few steps sd. One way to solve this probem coming
>>my mind is to fix Cl- during all the simulation (
>>including later production phase data collection).

The Cl- moving towards the protein !! Can you give a
order of magnitude of the movement of the Cl-. If it is
less that 2-3 ang it is ok. I guess you are using a 
The movement of Cl might just be a rearangment of its


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