VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 25 2005 - 19:32:08 CDT

It's pretty easy to add bonds actually to the psf file directly. See
the appendix of the NAMD tutorial for specifics on how the file is laid
out. Basically, you will have to adjust the numbers of bonds (noted at
the beginning of the bond section) and then add the two atoms you want
bonded. The bond length and force constant will take the form of that
for those specific atoms (defined in the parameter file).

To make the psf file in the first place, also see the NAMD tutorial, I
believe, for a description of this.

On Oct 25, 2005, at 7:16 PM, Craig Maloney wrote:

> Hi all.
>
> I'm currently using LAMMPS to do some MD simulations (not biological
> stuff per se). I'd like to manually tell VMD about bonds. I gather
> from traffic on this group that I cannot simply add "CONECT" lines to
> the pdb files, right? So my question is whether this can be done from
> the tcl or python interpreter? Or is there some documentation
> somewhere for what these "PSF" files are all about? Or what is the
> ETA for implementation in VMD of the CONECT lines feature?
>
> Thanks much,
> Craig