Ptraj actually does have a mechanic that checks if a second pass over
trajectories should be run. The actionInformation struct has a variable
called performSecondPass that is checked after the first round of trajectory
reads. If set, it calls ptrajProcessTrajectoryFiles again with the 4th arg
being PTRAJ_SECONDPASS as opposed to PTRAJ_ACTION (check near the end of
the ptraj() function in ptraj.c to see what I mean). So, you could have your
action do the coord averaging on the first pass, set performSecondPass to 1,
then do whatever is needed on the second pass.
-Dan
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
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 24 2010 - 19:00:06 PDT
