[gmx-users] NaCl force field with GROMOS 54A7

Thomas Piggot t.piggot at soton.ac.uk
Sun Oct 19 18:23:48 CEST 2014


For the ion parameters, I have seen the issue of forming salt crystals 
at relatively high concentrations (1M) (see 
http://redmine.gromacs.org/issues/773 for a few more details). The only 
paper I can remember reading which shows and discusses problems with the 
54A7/54A8 NaCl parameters being 'too sticky' is this one:


Regarding whether these issues means they 'should never be used', I 
think that this is quite an extreme statement. I would argue it depends 
upon how/why you are using them. Something along the lines of 'use them 
with caution' is probably more of an appropriate statement to make. I 
can't see, for example, how having one counter-ion used to neutralise a 
system would be a problem.



On 10/19/2014 04:12 PM, Jason Grosch wrote:
> Hello,
> I recently relieved a review which said that the NaCl force field of Reif
> and Hünenberger, included with the GROMOS 54A7 force field, has ions that
> are too sticky and therefore should never be used in conjunction with
> GROMOS 54A7. Could someone comment on the validity of this statement? I
> have not found much literature on the subject and would be grateful if you
> could point me in the correct direction.
> Also, are there any double counting issues centering a protein in a box 1
> nm from the box edge with a 1.4 Angstrom short-range cutoff? This would but
> the protein 2 nm from the nearest protein image and outside of direct
> interactions with each other. The box size in my simulations range from 15
> nm to 30 nm.
> Thank you for your time,
> Jason Grosch

Dr Thomas Piggot
University of Southampton, UK.

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