VMD-L Mailing List

From: Craig Maloney (cmaloney_at_kitp.ucsb.edu)
Date: Tue Oct 25 2005 - 20:05:04 CDT

Hi.

Which NAMD tutorial? Where can I find it?

Just to make sure: I'd like to generate a more or less "blank" psf
file (from my pdb file) and then add bonds to that file myself. Is
this the kind of thing that "psfgen" (which I read about in the NAMD
manual) will allow me to do?

Thanks.

--Craig

On Oct 25, 2005, at 5:32 PM, JC Gumbart wrote:

> 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
>>
>
>