Hi Dave
Thank you for your answer.
I have already tried to solvate in water my system, but I am studying
aggregation and so I would like to try to do some simulation in implicit
solvent, but until now I do not find how to build period box in implicit
solvent.
Elisa
2011/4/13 david condon <dec986.gmail.com>
> Hi Elisa,
>
> It is definitely doable. There are some tutorials online which show
> how to do this.
>
> However, implicit solvation is not particularly accurate. It is best
> to solvate in water. I use a truncated 8.65 A octahedron with TIP3P.
>
> -Dave
>
> On 4/13/11, Elisa Frezza <elisa.frezza.gmail.com> wrote:
> > Dear All
> >
> > I would like to ask you if I can perform MD simulation using implicit
> > solvation model and a cubic box to confine my systems.
> >
> > Your sincerely
> >
> > Elisa Frezza
> >
> > --
> > Elisa Frezza
> > Ph.D. Student in Material Science and Engineering
> > Dipartimento di Scienze Chimiche
> > Università di Padova
> > via Marzolo, 1
> > 35131 Padova - Italy
> > Phone: +39 049 827 5149
> > Emai: elisa.frezza.gmail.com
> > elisa.frezza.studenti.unipd.it
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
Elisa Frezza
Ph.D. Student in Material Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Wed Apr 13 2011 - 09:30:02 PDT
