From: Peter Freddolino (
Date: Thu Mar 05 2009 - 10:43:18 CST

Hi Nicola,
try using the -compound argument to pbctools, as described in the
documentation -- it lets you define portions of the structure that
cannot be wrapped separately from each pther.

Nicola Giacche' wrote:
> Hi Brittany,
> the problem is that when I use the pbc unwrap command in the whole
> trajectory, the results is a "broken" system with wrong bounds etc...
> then I would apply the command only to select frames... and for a
> trajectory of 5ns I can manually select the interval of "jumping" frames
> (I have about twenty intervals to select), but for longer trajectory I
> would like to use an automatic command or a script.
> If there is a command in vmd able to recognize, in the trajectory, the
> jumping frames it will be perfect for me. I will make a script with
> first the recognition of frames and then I will apply the pbc unwrap
> command only to the selected jumping frames.
> Does exist something like this?
> Nicola
> Hi Nicola,
> I am not sure. The way pcb unwrap works is that it bases it on the previous
> frame - if an atom moves more than a certain amount between frames, it
> assumes it has jumped. So if you wanted to avoid processing all of the
> frames, you could split up the trajectory into pieces with one normal frame
> before each of the jumping frames and process them individually. I am
> guessing that system size is the reason you don't want to process the whole
> trajectory together?
> Brittany
> -----Original Message-----
> From: Nicola Giacche' []
> Sent: Thursday, March 05, 2009 5:41 AM
> To: Brittany Morgan
> Subject: Re: vmd-l: script to resolve trajectory "jumps" on Desmond dynamic
> thank you Brittany, the command pbc unwrap -sel protein works, but now I
> have the problem to select only the frames that have "jumps"... is there
> in vmd an automatically command that select the "jumping" frames?
> for example: I know the coordinate limit value... then all frames with
> an atom over this value jump...
> thank you again
> Nicola
> Brittany Morgan ha scritto:
>> Hi Nicola,
>> I use 'pbc unwrap'.
>> Brittany
>> -----Original Message-----
>> From: [] On Behalf
> Of
>> Nicola Giacche'
>> Sent: Wednesday, March 04, 2009 11:15 AM
>> To: VMD Mailing-List
>> Subject: vmd-l: script to resolve trajectory "jumps" on Desmond dynamic
>> Hi,
>> I would to resolve a problem of Desmond dynamic... in some frames of the
>> dynamic, when an atom of the protein goes beyond the water-box, the
>> protein "jumps" to the next water-box... precisely, if the atom goes
>> beyond the Y direction, the component Y of the coordinates of the
>> protein "jumps" of value of the lenght Y of the water-box.
>> Is there a script on VMD able to restore the correct Y coordinates of
>> the protein (or chain), automatically, in the frames with the "jumps"?
>> thanks in advance,
>> Nicola