Re: namd2.7b1, tip4p, and dummies

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 30 2009 - 21:43:54 CDT

Hi Ed,
documentation on TIP4 will be included in the 2.7 release, but the code
is there in 2.7b1. I'll send you some sample files off list. I do not
expect the implementation in its present form to work with gromacs
formatted topologies; only charmm formatted. In 2.7b1 the only dummy
atom code is for the TIP4 (and related water model) lone pair, but some
more general code is currently in the works.

Best,
Peter

Edward Lyman wrote:
> Hi all,
>
> I have heard it said that namd can simulate 4 site water (tip4p, eg),
> and even read in gromacs formatted topology. But in the manual under
> the gromacs heading, it is mentioned that dummy atoms are not supported.
>
> Does this refer only to gromacs formatted inputs? ie, namd2.7b1
> supports dummy atoms, just not via gromacs inputs? And if this is the
> case, where else might I find a parameter file, namd ready, of
> tip4p/2005 ?
>
> Thx,
> Ed

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