[gmx-users] Performing MD simulations in presence of trivalent cations.

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 8 19:08:42 CEST 2014

On 2014-09-08 18:28, soumadwip ghosh wrote:
> Hello gmx users,
>                            I am currently working on the ion dependent
> persistence length calculations of RNA strands.I want to calculate it in
> presence of multivalent cations like Al3+ and Co3+. I guess in order to do
> that we have to include the specifications of these ions (either one) in
> the ions.itp file mentioned in the force field directory. My question is
> whether mentioning the charge +3 and giving a name (say Al) and mass of the
> ion would be sufficient enough for it or some other protocols are
> required.Also, is there any force field which will be suitable for such
> cations? I am not a professional in this field and any sort of help will be
> highly appreciated.
That's going to be really difficult. Present force fields have a lot of 
problems even with Mg2+ and Ca2+. In any way do you need to search the 
literature for Van der Waals (Lennard-Jones) parameters for such ions.
> Regards,
> Soumadwip

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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