Yes, I thought of this approach, and it may be the best one for a first
hands-on with the ptraj code :)
Many thanks, Ross.
On Mon, May 24, 2010 at 9:25 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jose,
>
> > I want to write a new action in ptraj that requires prior knowledge of
> > the
> > average coordinates. Is this possible in a single ptraj session? As I
> > understand the code, the trajectory is read only once and all requested
> > actions are performed on the current snapshot, as the "trajectory
> > pointer"
> > goes through the trajectory.
> > Since my action needs the average coordinates *a priori*, I need to
> > read the
> > trajectory twice. Can this be done in a single ptraj session?
>
> I believe that you would need to modify the code in order to support this
> as
> you describe it. However, the easiest approach might be to simply require a
> reference structure which your action uses and this reference structure is
> 'assumed' to be the average structure. One would then run ptraj to write a
> pdb of the average structure and then you run ptraj again to read this pdb
> file as the reference structure. This might be conceptually easier to
> implement even if it is not quite as clean with regards to how one runs it.
> This could be easily scripted though with a shell script calling both the
> ptraj runs, or even writing the necessary input files if needed.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Mon May 24 2010 - 19:00:05 PDT
