[gmx-users] genion-Cl

Nancy Deng jdeng at adrik.bchs.uh.edu
Fri Mar 4 01:42:16 CET 2005

Thank you  so much for the reply. The problem was  solved by rearranging the
Cl- location in the .gro file to make it match the location in the topology

----- Original Message ----- 
From: "X.Periole" <X.Periole at rug.nl>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, March 02, 2005 11:28 PM
Subject: Re: [gmx-users] genion-Cl

>> 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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