[gmx-users] restraining Ca2+ ion

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 7 02:21:30 CET 2009

jayant james wrote:
> Hi,
> Thanks for your suggestions. Please take a look at the mdp file that I 
> am using. Please suggest any changes that you feel would be adequate 
> if the electrostatic treatment is poor.

You're using cutoff electrostatics. That may have been a reasonable 
thing to do about 10+ years ago :-) It's well known that ionic solutions 
under cutoff electrostatics have artefacts in the radial distribution of 
ions - same charge ions have a peak just beyond the cutoff distance.

At the very least you should try using a reaction field, but probably 
PME is better. Also, like I implied last time, have a look at the 
chemistry of why these cations should be staying put. If there are more 
positively charged groups closer than negatively charged groups, then 
even distance restraints are not going to solve the problem in your 
model physics.


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