[gmx-developers] Problems with artificial minima when using soft-core potentials

[Shirts, Michael (mrs5pt)]

> Turning the electrostatics off completely first can add the the range of
> non-physical states that need to be sampled making the calculations
> slower and more complex than necessary.

My personal observation with this is that if it can be done in the same
simulation setup (which it can in 4.6), then it's better to do it in two
steps (coul then LJ), because all of these issues just disappear.  1 step
does not appear to be much if any less efficient that 2 step in general, as
the form of the dhdl curve generally less complicated
(http://dx.doi.org/10.1002/jcc.21909, Steinbrecher and Case).

I'd be interested to hear more about the problems that you're seeing.
Echoing Berk, his choice follows the Steinbrecher and Case suggestions,
which for ions means there will be no minima.  So I'm assuming that these
are more complicated molecules?  If so, how does one choose the right
combination of coul and vdw softcore?  Does it depend on the molecular
shape? It seems like it gets very complicated, and at a certain point, you
just bite the bullet in terms of having to potentially run 15 instead of 12
states and do it the simple way.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821



> Turning the electrostatics off completely first can add the the range of
> non-physical states that need to be sampled making the calculations
> slower and more complex than necessary.
> 
> Alpesh and I are writing a response to Bert's paper and a few other
> factors. I will send you a copy when we have a good draft.
> 
> Alan
> 
> 
> -- 
> --------------------------------------------------------------------
> This message was composed using voice recognition software. Please forgive any
> strange words I fail to correct.
> ____________________________________________________________________
> Prof. Alan E. Mark
> 
> BRISBANE
> Molecular Dynamics Group
> School of Chemistry and Molecular Biosciences (SCMB)
> University of Queensland
> Brisbane, QLD 4072,
> Australia
> 
> http://scmb.uq.edu.au/staff/alan-mark
> http://compbio.biosci.uq.edu.au
> 
> Physical address:
> Rm 331 Level 3, Molecular Biosciences Building (#76)
> 
> Email   a.e.mark at uq.edu.au
> Secretary:     md.secretary at uq.edu.au
> Phone:          +61-7-3365 4180
> FAX:            +61-7-3365 3872
> Secr:       +61-7-3365 3821
>                  
> Unless stated otherwise, this e-mail represents only the views of the Sender
> and not the views of The University of Queensland
> 
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.