Re: OPC Water Model

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jun 24 2019 - 09:06:32 CDT

Peter's advice is good.

The rigid water heuristics are fairly robust as long as you don't futz with
mass. If rigidBonds is water or all and waterModel is tip4, then any 4 atom
residue where the first atom is oxygen and the third and fourth atoms are
hydrogen (all based on mass cutoffs) will be rigid based on the bond
parameters. I'm not 100% what happens with the lonepair for amber inputs,
so of things look wonky go ahead ans send me inputs offline and I'll take a
look.

HTH,
BKR

On Mon, Jun 24, 2019, 8:18 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> Off the top of my head, it seems like this *should* work as long as you
> also have rigidbonds set to 'all'. But I don't recall whether the rigid
> water code path will properly harvest the geometry from an amber prmtop
> file, so you ought to run dynamics for a bit and then confirm that the
> proper geometry is being maintained, and then as long as it is, do some
> basic testing (eg, density of a pure water box in NPT simulation) to make
> sure that you match the values from the paper. Note that the geometry *will
> not* be constrained during minimization, so you actually need to run a few
> steps of dynamics to make sure that it is working.
> Best,
> Peter
>
> On Mon, Jun 24, 2019 at 6:54 AM eee ffff <elinovemail_at_abv.bg> wrote:
>
>> Dear NAMD Experts,
>>
>> I would like to use the OPC water model in namd. For this purpose, I
>> selected the option waterModel tip4 and a prmtop/parm7 file with the OPC
>> water parameters. Is this the right approach?
>>
>

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