Re: Strange vdw_dU/dl values in thermodynamic integration

From: Floris Buelens (
Date: Fri Oct 22 2010 - 01:36:45 CDT

When applying a soft-core potential the derivative is no longer a linear
function of lambda. The VDW potential should be equal to dU/dl if you set
alchVdwShiftCoeff to 0, which reduces the soft core potential back to linear
scaling of Lennard-Jones.

----- Original Message ----
From: Hugh Heldenbrand <>
Sent: Fri, 22 October, 2010 2:37:25
Subject: namd-l: Strange vdw_dU/dl values in thermodynamic integration


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
rigidTolerance 0.0005
cutoff 10
switching off
amber on
exclude scaled1-4
1-4scaling 0.833333

Although in this case there aren't any 1-4 terms or rigid bonds.

Here are the TI settings that I used:

alch on
alchType ti
alchLambda 0.00
alchLambda2 0.00
alchFile ./namd_data/cc.pdb
alchCol B
alchOutFreq 1
alchOutFile ti_out
alchVdwShiftCoeff 5
alchVdwLambdaEnd 0.5
alchElecLambdaStart 0.5

Am I misunderstanding TI vdw interactions or is this a bug?

-Hugh Heldenbrand
University of Minnesota


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