From: Hugh Heldenbrand (helde010_at_umn.edu)
Date: Fri Oct 22 2010 - 07:28:05 CDT
Thank you, Floris, for you quick response.
But the soft-core potential should be equal to the "regular"
Lennard-Jones potential at lambda = 0, shouldn't it? The initial
two-atom example I gave was for lambda = 0.
Also, at lambda = 1, the soft-core potential should be 0, shouldn't it?
For the two-atom example I just gave, I get a VDW potential of 0 in the
output file, but a non-zero vdw_dU/dl.
Finally, turning off the soft-core potential (setting alchVdwShiftCoeff
= 0) does indeed give a vdw_dU/dl equal to the VDW potential from the
output file for lambda = 0. But it gives the same vdw_dU/dl for all
other values of lambda that I tried. Shouldn't setting lambda = 1 give
a vdw_dU/dl equal to 0 in this case?
University of Minnesota
On 10/22/2010 01:36 AM, Floris Buelens wrote:
> 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<helde010_at_umn.edu>
> To: namd-l_at_ks.uiuc.edu
> 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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