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
