how does NAMD know which residue to (de)couple

From: Qasim Pars (qasimpars_at_gmail.com)
Date: Sun Jun 21 2020 - 17:28:19 CDT

Next message: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Previous message: Indrajit Deb: "Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ..............."
Next in thread: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Reply: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear users,

Please look the input file in this free energy tutorial:
https://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/ABF-tutorial-files/Methane-Hydration/FEP/decouple-forward.conf
How does NAMD know which residue to (de)coupled during the hydration free
energy calculation? Note that it's the first residue in the tutorial.

If I want to decouple the third residue in the psf/pdb for the solvation
free energy calculation, what should I do in the input file? ( that is, I
want to calculate the solvation free energy of the third residue).

Any help will be appreciated.

Thanks,

-- 
Qasim Pars

Next message: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Previous message: Indrajit Deb: "Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ..............."
Next in thread: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Reply: Michael Robinson: "Re: how does NAMD know which residue to (de)couple"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST