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/
> --
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 25 2011 - 04:00:04 PST
