[gmx-users] Regarding MD simulations involving metal ion (Mn)

Paul bauer paul.bauer.q at gmail.com
Wed May 16 12:11:50 CEST 2018


for metal ions (and especially transition metals) you should first 
consider what kind of metal model you want to employ, as the different 
models (bonded, soft sphere or dummy model) have have different properties.
There are numerous papers outlining the parametrization of those 
different models, so you can search them once you have decided on how 
you want to model the ion :)

If you are in need of modelling things such as unpaired electrons, spin 
effects or anything else quantum mechanical, you should consider if MD 
is the correct approach to simulate a structure like this or if a pure 
QM description is more appropriate.

If you have a reference for a similar system you should follow the 
approach outlined there as much as possible.

Also one note of caution, you should only use one force field to 
simulate your system, and never mix and match force fields.



On 16/05/18 11:57, dhaval patel wrote:
> Dear All,
> I need to simulation of protein-ligand with coordinated metal ion bound to
> ligand. The metal ion is Mn+2, Advise me whether its correct to use
> CHARMM36 and OPLSS force field for parameterization? What things should
> taken care while simulating such cases where we have metals with unpaired
> electrons?   Any help is  highly appreciated.
> Sincerely yours,
> ​Dhaval​

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