VMD-L Mailing List

From: Andrei A Golosov (agolosov_at_fas.harvard.edu)
Date: Fri Mar 10 2006 - 12:17:50 CST

Thanks, John!

Here is a little piece of code (in fortran) that could clarify the
format

INTEGER NCLX,NCLY,NCLZ
REAL*8 DCEL
REAL*8 XBCEN,YBCEN,ZBCEN,EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM

attention:
REAL*4 data(mxgrid*mxgrid*mxgrid) this is like float
and notice how the data is looped (z grid changes the fastest)

      open (unit = 33, file = 'phi.dat',form='unformatted')
      read (33) NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN
      if ( ( nclx .gt. mxgrid ) .or. ( ncly .gt. mxgrid ) .or.
     $ ( nclz .gt. mxgrid) ) then
         print *,'exceed maximum allowed grid'
         stop
      endif
      read (33) EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM
      read (33) (data(i),I=1,NCLX*NCLY*NCLZ)
      close(33)
      print *, 'NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN are'
      print *,NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN
      print *,'EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM are'
      print *,EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM
      xmin = -dcel*(NCLX - 1)/2
      ymin = -dcel*(NCLY - 1)/2
      zmin = -dcel*(NCLZ - 1)/2
      xmax = -xmin
      ymax = -ymin
      zmax = -zmin
      print *,'xmin, ymin, zmin'
      print *, xmin, ymin, zmin
      icnf = 1
      do i = 1, NCLX
         do j = 1, NCLY
            do k = 1, NCLZ
               phi(i,j,k) = data(icnf)
               icnf = icnf + 1
            enddo
         enddo
      enddo

---Andrei

On Fri, 10 Mar 2006, John Stone wrote:

>
> Andrei,
> The volumetric grid formats read by VMD (minus a couple of the newest
> ones which I'll add to the docs later today) are listed here:
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
>
> If someone has documentation on the precise format that Charmm uses,
> it wouldn't be hard to write a VMD plugin to read them.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Mar 10, 2006 at 11:52:14AM -0500, Andrei A Golosov wrote:
> > Hi, John!
> > In which format vmd takes electrostatic potential, perphaps I could make
> > CHARMM to make it in vmd way.
> > Thanks.
> > ---Andrei
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>