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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Received on Fri Aug 12 2011 - 10:30:03 PDT
