Re: simulation box

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Fri May 20 2011 - 11:36:57 CDT

You don't. There is no "solvate" command in NAMD.

Perhaps you mean VMD? If so, you can use "Extensions-> Modeling ->Add
Solvation Box". In this tool you can set your box size to whatever you
want it to be.

PAUL NEWMAN wrote:
> Hello,
> I want to set up the size of my simulation box and also center my
> protein. Let's say in x=100; in y=200 and z=50. How can I do that by
> using the commands inside NAMD like solvate.
>
> Thanks
>
> On Fri, May 20, 2011 at 12:25 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Fri, May 20, 2011 at 12:11 PM, PAUL NEWMAN
> <paulclizana_at_gmail.com <mailto:paulclizana_at_gmail.com>> wrote:
> > Thanks for the information; but are there any other way using
> just the
> > commands inside NAMD.
>
> paul,
>
> your question is not very clear.
>
> you have to explain in more detail as to what
> commands exactly you are referring to and
> what it is exactly that you want to different and why.
>
> please reformulate your question and your
> chances of getting a useful answer will improve.
>
> cheers,
> axel.
>
>
>
> > Thanks
> >
> > 2011/5/20 Marek Maly <marek.maly_at_ujep.cz
> <mailto:marek.maly_at_ujep.cz>>
> >>
> >> Hi,
> >> I am not an expert on NAMD (I am AMBER user) but one
> alternative for you
> >> might be to create your simul. box outside for example using
> PACKMOL
> >>
> >> http://www.ime.unicamp.br/~martinez/packmol/
> <http://www.ime.unicamp.br/%7Emartinez/packmol/>
> >>
> >> Best,
> >>
> >> Marek
> >>
> >>
> >>
> >> Dne Fri, 20 May 2011 17:39:48 +0200 PAUL NEWMAN
> <paulclizana_at_gmail.com <mailto:paulclizana_at_gmail.com>>
> >> napsal/-a:
> >>
> >>> Hi,
> >>> I would like to know how to set up the size of the simulation
> box in
> >>> NAMD. I
> >>> want to set up X Y and Z. I dont want to use the one give by NAMD
> >>>
> >>> Thanks for the help
> >>>
> >>> Paul
> >>>
> >>>
> >>>
> >>> __________ Informace od ESET NOD32 Antivirus, verze databaze 6138
> >>> (20110520) __________
> >>>
> >>> Tuto zpravu proveril ESET NOD32 Antivirus.
> >>>
> >>> http://www.eset.cz
> >>>
> >>
> >>
> >> --
> >> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> >> http://www.opera.com/mail/
> >
> >
> >
> > --
> > Cheers,
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>
>
> --
> Cheers,
>
> Paul
>
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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