From: Hugh Heldenbrand (helde010_at_umn.edu)
Date: Thu Oct 21 2010 - 19:37:25 CDT
I am attempting to do thermodynamic integration calculations using
parameter and coordinate files in the AMBER format. Some of the
vdw_dU/dl values that I was getting seemed strange, so I did a test on
two isolated atoms with zero charge and the vdw parameters for the C
atom type from the AMBER parm99 forcefield. In my test the two atoms
are separated by three angstroms and I decouple one of them. My
understanding is that for a lambda value of 0 the two atoms should
interact fully with a vdw_dU/dl value equal to their VDW potential energy.
However, in my output file the VDW potential energy is 0.8144, and the
vdw_dU/dl is 4.7432 for the 0th timestep.
Here are the settings that I use to make NAMD AMBER forcefield compatible:
# AMBER settings
Although in this case there aren't any 1-4 terms or rigid bonds.
Here are the TI settings that I used:
Am I misunderstanding TI vdw interactions or is this a bug?
University of Minnesota
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