[AMBER] Velocity autocorrelation

From: ATUL KUMAR <atul44_sit.jnu.ac.in>
Date: Wed, 7 Jun 2017 16:52:37 +0530

Dear amber user,
I am trying to calcualte velocity autocorrelation of some water molecules
around some specific atom of DNA. the cpptraj command i am using is gives as
parm md.prmtop
trajin md.nc mdvel .md.mdvel
autoimage
rms first :1-46 out rms.out
velocityautocorr VELOCITY :1890.O,:34530.O,:10532.O usevelocity out
vel_auto_cor.out tstep 0.1 norm

but the output i am getting from this does not seems meaningful to me. Can
anyone help me with this.

the output file is like this:

#Frame VELOCITY
      1.0000 1.0000
      1.1000 0.0560
      1.2000 -0.0096
      1.3000 -0.0319
      1.4000 -0.0298
      1.5000 -0.0147
      1.6000 -0.0084
      1.7000 -0.0053
      1.8000 -0.0030
      1.9000 -0.0033
      2.0000 -0.0019
      2.1000 -0.0005
      2.2000 0.0002
      2.3000 -0.0030
      2.4000 -0.0016
      2.5000 -0.0014
      2.6000 -0.0012
      2.7000 0.0001
      2.8000 -0.0004
      2.9000 0.0014
      3.0000 -0.0000
      3.1000 -0.0002
      3.2000 -0.0009
      3.3000 0.0005
      3.4000 -0.0002
      3.5000 0.0009
      3.6000 -0.0001
      3.7000 0.0015
      3.8000 -0.0031
      3.9000 -0.0036
      4.0000 -0.0001
      4.1000 0.0010
      4.2000 -0.0008
      4.3000 -0.0018


for detailed output kindly see the attachment

thank you
*Atul Kuamr jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU,New Delhi
India.


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Received on Wed Jun 07 2017 - 04:30:02 PDT
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