From: Yue Qian (tiantianqyqy_at_gmail.com)
Date: Mon Jun 20 2016 - 17:09:04 CDT
Dear NAMD users,
I am currently using NAMD to carry out free energy of binding calculations
of a protein-ligand system. I have encountered several problems regrading
the long-range LJ corrections. I have googled for certain issues but
couldn't find relevant, informative discussions.
This is what I found on the manual:
LJcorrection: Description: Apply an analytical correction to the reported
vdW energy and virial that is equal to the amount lost due to switching and
cutoff of the LJ potential. The correction will use the average of vdW
parameters for all particles in the system and assume a constant,
homogeneous distribution of particles beyond the switching distance. See
 for details (the equations used in the NAMD implementation are
slightly different due to the use of a different switching function).
Periodic boundary conditions are required to make use of tail corrections.
LJcorrection as implemented is inconsistent with vdwForceSwitching.
Here are my questions:
1. To turn on the long-range LJ correction, is "LJcorrection yes" is the
only thing I need to do? (From the manual, I noticed that "LJcorrection as
implemented is inconsistent with vdwForceSwitching." vdwForceSwitching was
kept off.) I have tested this protocol in unbound state calculation with
only the solute molecule and TIP3 water molecules with LJcorrection on and
off. However, I did not observe significant difference, which was expected
to be around 0.5 ~ 0.6 kcal/mol. But with "Ewald off", the calculation
result was ~0.8kcal/mol more positive. This patten applies to different
cutoffs, from 8 Ang to 12 Ang.
2. According to the manual, the LJcorrction option assumes a homogeneous,
isotropic environment which only applies to unbound state calculation. To
be able to apply to bound state calculation, heterogenous, nonisotropic
environment needs to be considered. The cited paper (J. Phys. Chem. B, Vol.
111, No. 45, 2007) covered both scenarios. But GROMACS was used in their
work. I was wondering if there's anyway to incorporate such methods in NAMD.
Any clue is appreciated. Thank you very much.
-- Yue Qian
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:33 CST