Vijay - the "diffusion" command is for translational diffusion. You want to
look at rotdiff command and its documentation to get the rotational
diffusion tensor. A number of 500 random vectors should suffice to get
converged results.
Let us know how that works for you.
George
On Fri, Mar 29, 2013 at 7:11 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear Sir,
>
> I would like to calculate
>
> The script I used to calculation diffusion is as blow
>
> #!/bin/bash
>
>
> TRAJfolder="/home/vijay/Simulation-Folder-Feb2013/TRAJECTORY-thermo-system/malto-thermo-traj"
>
>
> cpptraj $TRAJfolder/malto-THERMO.top << EOF
>
>
> trajin $TRAJfolder/malto-thermo.set11.traj
>
> trajin $TRAJfolder/malto-thermo.set12.traj
> trajin $TRAJfolder/malto-thermo.set13.traj
> trajin $TRAJfolder/malto-thermo.set14.traj
> trajin $TRAJfolder/malto-thermo.set15.traj
> trajin $TRAJfolder/malto-thermo.set16.traj
> trajin $TRAJfolder/malto-thermo.set17.traj
> trajin $TRAJfolder/malto-thermo.set18.traj
> trajin $TRAJfolder/malto-thermo.set19.traj
> trajin $TRAJfolder/malto-thermo.set20.traj
>
> diffusion .DDM 5.0 average diff_malto_thermo.dat
> exit $?
>
> EOF
>
> ********************************************************************
> Now I am trying to calculate rotational diffusion for my lipids in
> bilayer, where C2 and C5 would be my vector parallel to bilayer surface.
> (my system is sugar - glucose)
>
> I understand that I need to modify the above script to run my rotational
> calculation by defining the vectors. But I feel like lost in declaring the
> vectors.
>
> Could someone help me here?
>
> Thank you in advance.
> Vijay
>
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 29 2013 - 06:30:03 PDT
