Hi Dr Roe,
Thanks for the reply. I only have the coordinate trajectory and not the
velocity trajectory. But when I run ptraj with the following input file
trajin amn1122_xd1_umbrella.mdcrd
vector v1 :993.CG :996.N out 1122.vector
In the output file 1122.vector I get
# FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
# FORMAT where v? is vector, c? is center of mass...
1 3.0480 -3.3340 0.5420 39.0820 74.6050 82.5470 42.1300 71.2710
83.0890
2 3.0760 -3.1120 0.3820 38.9750 74.4530 82.7710 42.0510 71.3410
83.1530
3 2.6490 -3.5640 0.2170 38.7760 74.9080 82.7360 41.4250 71.3440
82.9530
4 3.1760 -3.6330 0.6680 38.4630 74.7350 82.4500 41.6390 71.1020
83.1180
5 3.0710 -3.4880 0.5020 38.5650 74.7810 82.5050 41.6360 71.2930
83.0070
6 2.5780 -3.4220 0.3740 38.7850 74.9910 82.6530 41.3630 71.5690
83.0270
..........................................
..........................................
I know that there is only coordinate information in the mdcrd file. So what
do these vx vy and vz represent?
Thank you
Sajeewa Dewage
On Fri, May 17, 2013 at 1:34 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, May 17, 2013 at 11:05 AM, Sajeewa Pemasinghe
> <sajeewasp.gmail.com> wrote:
> > vector vectorforall :* :*
>
> This vector is going to be 0.0. You are saying take the vector from
> the COM of all atoms to the COM of all atoms. If you want the average
> velocity of all atoms in a residue (assuming you are reading in a
> velocity trajectory instead of coordinates) you would need something
> like this for every residue:
>
> vector res1V center :1
> vector res2V center :2
> ...
>
> I think this will only work with cpptraj since ptraj requires a second
> mask for 'corr' vectors. For ptraj you could *maybe* get away with
> specifying all atoms for the second mask, but I'm not sure if the
> autocorrelation function will be calculated correctly in that case.
>
> Once you have the vectors you can calculate the autocorrelation
> function for each vector with 'timecorr'. As always please read the
> manual on the related commands carefully so you understand exactly
> what they are doing. It may be useful to try your calculations on a
> limited number of frames first and see if the results make sense to
> you.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
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Received on Fri May 17 2013 - 11:30:04 PDT
