Hi,
My guess is that you want to look at only the water oxygens instead of
oxygen and hydrogen (i.e. :WAT.O instead of :WAT).
-Dan
On Sun, Nov 3, 2019 at 1:00 PM Ajeet Kumar Yadav <ajtyadav1997.gmail.com> wrote:
>
> 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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Received on Mon Nov 04 2019 - 11:30:02 PST
