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From: Sujata Sovani (sujatas_at_scripps.edu)
Date: Wed Jul 29 2009 - 12:10:09 CDT
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Hi All,
I am new to NAMD.
I am following the tutorial using my molecule. I have solvated the protein and moving onto minimization and equilibration.
In the configuration file http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node9.html
in the Simulation parameters, the FF parameters to be excluded in the 'ub_ws_eq.conf file' are:
exclude scaled1-4
Are scaled 1-4 always to be excluded? If yes why? what are the other options?
Thank you.
Regards,
Sujata
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