Date: Sun, 3 Nov 2019 23:30:28 +0530
Dear Amber Users,
I am trying to calculate velocity auto-correlation function by
"velocityautocorr" function in cpptraj.
For this, I have combined my trajectory coordinate file (.nc) and
velocity information file(.mdvel) using the command:
*parm sys.prmtoptrajin prod10ps.mdcrd mdvel prod10ps.mdveltrajout
crd_vel10ps.nc <http://crd_vel10ps.nc>*
Then calculating velocity auto-correlation function by using the
commond:
*parm sys.prmtoptrajin crd_vel10ps.nc <http://crd_vel10ps.nc> mdvel
prod10ps.mdvelvelocityautocorr :WAT usevelocity out velocity_corr_wat10ps
maxlag 10 tstep 0.001 norm*
I tried to reproduce the paper "Computing the Self-Diffusion Coefficient
for TIP4P Water" by "D. V. Zlenko".
But I am getting different result from paper ( one extra minimum ), I have
attached the plots of paper(paper.png)(figure 3b of the paper) and my
calculation(cpptraj_vacf.png).
Please help me to fix this problem.
I will be very thankful if anyone tells me what mistake I am making in
the calculation.
-- *WITH REGARDS* *------------------------------------------------------------------------------------------* *AJEET KUMAR YADAV* *STUDENT* *SCHOOL OF COMPUTATIONAL AND INTEGRATIVE SCIENCES* *JNU, NEW DELHI (110067) *
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(image/png attachment: paper.png)
(image/jpeg attachment: cpptraj_vacf.jpg)
