[gmx-users] Polarisable water topology / Ions

Paul van Maaren maaren at home.nl
Sat Mar 11 13:28:56 CET 2006

+++ Maxim Fedorov [Fri, Mar 10, 2006 at 07:56:49PM +0000]:
> 1. Does anybody have a 'ready-to-run' topology
> for SW water (the polarisable water model from J.Phys. Chem. B (2001),
> 105, 2618? 
> As I see the sw.itp in the standart distribution
> has improper order of directives. Am I right or it is just the Friday
> night and I should take a rest for a while...? 
> But
> the grompp also tells me:  "Invalid order for directive defaults, file
> ""/home/users/mfedorov/utils/gromacs/share/gromacs/top/sw.itp"", line 35
> I am able to prepare this topology by myself but it would cost me some
> time. And I can also make a mistake - I am a human being at the end ...
> Is there a good soul which help me to save this bit of my life-time? If
> somebody has a box of the sw - water I'll tell him many-many thanks as well.

It works for me for small clusters, I ahvenot done bulk simulations recently. 
If you are still having problems, send me
your files off list and I will take a look. I can also provide you with
boxes, just let me know the size you are looking for.

> 2. Can anybody give me a piece of advice about ion parameters which work
> more or less well for SW? I would appreciate 
> any link for literature or just parameters.

The most recent shell-model ion parameters are:

  author =       {G. Lamoureux and B. Roux},
  title =        {Absolute Hydration Free Energy Scale for Alkali and
                  Halide Ions Established from Simulations with a
                  Polarizable Force Field},
  journal =      BTjpcb,
  year =         2006,
  volume =       117,
  pages =        {3308--3322},
  OPTabstract =  {},
  OPTnote =      {},
  OPTurl =       {http://dx.doi.org/10.1021/jp056043p}

But I have not tested them with SW...


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