**From:** Hugh Heldenbrand (*helde010_at_umn.edu*)

**Date:** Fri Oct 22 2010 - 07:28:05 CDT

**Next message:**Jim Phillips: "Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value)."**Previous message:**oguz gurbulak: "potential functions in NAMD"**In reply to:**Floris Buelens: "Re: Strange vdw_dU/dl values in thermodynamic integration"**Next in thread:**Floris Buelens: "Re: Strange vdw_dU/dl values in thermodynamic integration"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello-

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?

-Hugh Heldenbrand

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
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*> function of lambda. The VDW potential should be equal to dU/dl if you set
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*> alchVdwShiftCoeff to 0, which reduces the soft core potential back to linear
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*> scaling of Lennard-Jones.
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*>
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*>
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*>
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*>
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*> ----- Original Message ----
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*> From: Hugh Heldenbrand<helde010_at_umn.edu>
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*> To: namd-l_at_ks.uiuc.edu
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*> Sent: Fri, 22 October, 2010 2:37:25
*

*> Subject: namd-l: Strange vdw_dU/dl values in thermodynamic integration
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*>
*

*> Hello-
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*>
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*> I am attempting to do thermodynamic integration calculations using parameter and
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*> coordinate files in the AMBER format. Some of the vdw_dU/dl values that I was
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*> getting seemed strange, so I did a test on two isolated atoms with zero charge
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*> and the vdw parameters for the C atom type from the AMBER parm99 forcefield. In
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*> my test the two atoms are separated by three angstroms and I decouple one of
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*> them. My understanding is that for a lambda value of 0 the two atoms should
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*> interact fully with a vdw_dU/dl value equal to their VDW potential energy.
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*>
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*> However, in my output file the VDW potential energy is 0.8144, and the vdw_dU/dl
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*> is 4.7432 for the 0th timestep.
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*>
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*> Here are the settings that I use to make NAMD AMBER forcefield compatible:
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*>
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*> # AMBER settings
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*> rigidTolerance 0.0005
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*> cutoff 10
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*> switching off
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*> amber on
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*> exclude scaled1-4
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*> 1-4scaling 0.833333
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*>
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*> Although in this case there aren't any 1-4 terms or rigid bonds.
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*>
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*> Here are the TI settings that I used:
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*>
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*> alch on
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*> alchType ti
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*> alchLambda 0.00
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*> alchLambda2 0.00
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*> alchFile ./namd_data/cc.pdb
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*> alchCol B
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*> alchOutFreq 1
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*> alchOutFile ti_out
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*> alchVdwShiftCoeff 5
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*> alchVdwLambdaEnd 0.5
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*> alchElecLambdaStart 0.5
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*>
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*> Am I misunderstanding TI vdw interactions or is this a bug?
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*>
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*> -Hugh Heldenbrand
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*> University of Minnesota
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*>
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*>
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*>
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**Next message:**Jim Phillips: "Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value)."**Previous message:**oguz gurbulak: "potential functions in NAMD"**In reply to:**Floris Buelens: "Re: Strange vdw_dU/dl values in thermodynamic integration"**Next in thread:**Floris Buelens: "Re: Strange vdw_dU/dl values in thermodynamic integration"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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