Hi Ilyas,
I have always used the first formulation mentioned by you and it
worked.
Even though I think they are equivalent: as far as I can recall the
truncated octahedron box has the property to be invariant to several
transformations.
I am not sure about which ones though...
By the way you can check which formulation is correct by running a
very short (even one step,
just to obtain your filename.restart.xsc) constant volume simulation
(or minimisation) with
NAMD, using both formulations.
Then you can display the initial *Amber files* in VMD and setting the
box info with the XSC
file you obtained using the following command in the Tk console:
% pbc readxst filename.restart.xsc
If ticking the +/-x, +/-y and +/-z Periodic images in Graphic -> Representation
the resulting images correspond with one another, your simulations should
be fine.
Good luck,
M
On 1 March 2013 00:32, Ilyas Yildirim <i-yildirim.northwestern.edu> wrote:
> I've checked out the mailing list and web regarding this, and there is
> the following document in amber website on this matter.
>
> http://ambermd.org/namd/namd_amber.html
>
> For getting the right cellbasisvectors to use in NAMD for a system in
> Truncated Octahedron (TO), there is a formulae in this website.
>
> cellBasisVector1 d 0.0 0.0
> cellBasisVector2 (-1/3)*d (2/3)sqrt(2)*d 0.0
> cellBasisVector3 (-1/3)*d (-1/3)sqrt(2)*d (-1/3)sqrt(6)*d
>
> Is the last term for cellBasisVector3 correct? There is a script in ub.edu
> written in perl (called amber2namd.pl) that created namd input files from
> amber prmtop/inpcrd files, and in this script the last term is positive;
> namely (+1/3)sqrt(6)*d.
>
> Can anyone having an experience on using amber files in namd simulations
> comment on this? Thanks.
>
> Best,
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
http://www.iecb.u-bordeaux.fr/
Emails: m.porrini.iecb.u-bordeaux.fr
M.Porrini.ed.ac.uk
maxp.iesl.forth.gr
mozz76.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 01 2013 - 02:30:02 PST
