Hi,
The trajectory format actually contains only coordinates, not
velocities (restart files are the ones that include both). Box info is
included only if your system is periodic. If you want ptraj to not
print box information to a trajectory use the 'nobox' keyword, i.e.:
trajin mdcrd
trajout output.crd nobox
For more specific information on the coordinate trajectory format see
"
http://ambermd.org/formats.html#trajectory". Hope this helps.
-Dan
On Fri, Feb 25, 2011 at 6:31 AM, siddesh southekal
<siddeshonline.gmail.com> wrote:
> Thanks for the reply.
> i followed your 2nd suggestion : trajout the protein using mask and analyse
> the com of coordinates
> i encounter a small problem here-
> i read in other mailing lists about the trajout format : (X(i), Y(i), Z(i),
> i = 1,NATOM). followed by the velocity and box information.
> Is there a way i can strip this information and have only the coordinates
> for entire trajectory / or how do i know from where the velocity and box
> information begins so that i can omit them ?
> so basically my program -
> 1. extracts the coordinates (example x coordinate) : x(i)..x(NATOM)
> 2.then groups for each frame or time step ( as i think trajout file contains
> : x(1)..x(NATOM) at frame1 1followed by x(1)..x(NATOM) at frame2 ..or am i
> wrong ?! )
> 3.calculates the com of coordinates
>
> Thanks for the help again ,
> Sid
>
> On Fri, Feb 18, 2011 at 3:57 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
>
>> As far as I know, you can't directly output the center of mass trajectory.
>> Thus, there are three options I can think of:
>> 1) Pick an atom that stays near the center of the (protein?) and print out
>> that trajectory.
>> 2) Use ptraj to trajout the protein only using a mask, then make your own
>> program to analyze the com of the coordinates.
>> 3) Do you need to know the full trajectory? Usually people care more about
>> the distance along the vector normal to the membrane. In this case, look up
>> the vector command in ptraj in the ambertools manual.
>>
>> --Dan
>>
>> On Thu, Feb 17, 2011 at 10:09 PM, siddesh southekal <
>> siddeshonline.gmail.com
>> > wrote:
>>
>> > Hello all,
>> > I have a system containing protein, lipids and solvent
>> > I want to compute the motion of center of mass along the simulation
>> > trajectory of the protein.
>> > Is this possible using ptraj ? Can anybody give me an idea how i can do
>> > this
>> > ?
>> >
>> > sid
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Dr. Daniel J. Sindhikara
>> Institute for Molecular Science
>> E-mail: sindhikara.gmail.com
>> Website: http://sites.google.com/site/dansindhikara/
>> --
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Feb 25 2011 - 04:30:02 PST
