Dan,
I can definitely do that. Should I think about making both boxes larger to
start out with (perhaps 12.0), so that when I remove the extra waters, both
will still be solvated in a sufficiently large box? I just don't want to run
into any artifacts caused by not having enough of a buffer between the
solute and the edge of the box. Also, is there a way to ensure that the
waters are removed in a way that maintains the geometry of the box?
Adieu,
Will
On Fri, Aug 12, 2011 at 1:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Aug 12, 2011 at 8:52 AM, William Cantara <wcantara.gmail.com>
> wrote:
> > If this is correct, do I stand to create any artifacts in my simulation
> by
> > simply using the .prmtop file that contains the larger octahedral water
> box?
>
> You will definitely have a problem if you use a prmtop that has a
> different number of atoms than the corresponding coordinate file; you
> need to make sure your coordiantes match your topology.
>
> I think an easier procedure might be when you generate the larger box
> with leap, use the "remove" command to delete as many waters as
> necessary so that it matches the smaller system. Make sure you
> carefully equilibrate both endpoint systems (especially if you have
> deleted some waters) before you run NEB.
>
> Good luck!
>
> -Dan
>
> >
> > Thank you in advance for your help!
> >
> > Adieu,
> >
> > Will Cantara
> >
> > Graduate Student, North Carolina State University
> > Research Project Asst., The RNA Institute, SUNY Albany
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> >
>
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Received on Fri Aug 12 2011 - 12:00:02 PDT
