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
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Received on Fri Mar 29 2013 - 04:30:02 PDT
