[CPMD-list] (no subject)

[Axel Kohlmeyer]

On 11/19/07, kdong <kdong_bj at sina.com> wrote:

> Dear everyone,
>   I want to study the breaking and forming of chemical bonds by metadynamics
> in CPMD-3.11, but now I am very layman for metadynamics, especially the
> collective variables. so I have a few of questions for metadynamics as
> follows,
>   1. how to set up the index of atoms in  the implemented types of CV, for
> example "DIST: Distance between two atoms: give the indexes of the 2 atoms
> i1 i2, s = di1,i2.", is it the sequence of atoms in &ATOM......&END section.

collective variables are similar to constraints, so the identification of
atoms is the same. the index is the position of the atom in the GEOMETRY
file, which is determined by the ordering in the &ATOM section, as you
already estimated.

>  2. how to display and deal with the outfile with extension "_mtd" by
> visual software, for example VMD.

those files represent the evolution of various parameters during the
metadynamics. they are _not_ coordinates, so there is no point
to read them into VMD. IIRC, there is a program in the contrib section
of the www.cpmd.org download area that will help reconstruct the free
energy profile for the output of that (and most of the others) you should
be fine with gnuplot and/or xmgrace.

>  It is appreciated if you can give many suggestions about metadyanics.

read the manual, the MTD section is extensive, there are commented
examples in the CPMD-test distribution, and check out the MTD papers.
cheers,
   axel.

>
>
>
> 2007-11-19
>  ________________________________
>
> K. dong
> Institute of Process Engineering
> Chinese Academy of Sciences
> P. O. BOX 63, Beijing 100080
> The People's Republic of China
> E-mail: dongkun at home.ipe.ac.cn
>           kdong at foxmail.com
>  ________________________________
>
>
>
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>
>


-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.