From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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.
Peter

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' [mailto:nicolag_at_chimfarm.unipg.it]
> 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'.
>>
>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>
>> Brittany
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] 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
>>
>>
>