AMBER Archive (2008)

Subject: Re: AMBER: interaction energies in Amber and VMD/NAMD

From: Alan (
Date: Sun Jul 27 2008 - 01:26:32 CDT


Have you looked at

Pay well attention to:

3. NAMD has several exclusion policy options, defined by exclude. The
way AMBER dealing with exclusions corresponds to the ``scaled1-4'' in
NAMD. So for simulations using AMBER force field, one would specify
``exclude scaled1-4'' in the configuration file, and set 1-4scaling to
the inverse value of SCEE as would be used in AMBER.

5. By default, NAMD applies switching functions to the non-bond
interactions within the cutoff distance, which helps to improve energy
conservation, while AMBER does not use switching functions so it
simply truncates the interactions at cutoff. However, if ``authentic''
AMBER cutoff simulations are desired, the switching functions could be
turned off by specifying ``switching off'' in NAMD configuration file.

and check those parameters in your namd.conf file:
1-4scaling 0.833333 # =1/1.2, default is 1.0
scnb 2 # This is default
switching off # Turn off the switching functions, try on also
readexclusions yes #you may compare with 'no' too.

And , as David ask, how much is the difference in percentage?


On Sun, Jul 27, 2008 at 1:46 AM, Carlos Simmerling
<> wrote:
> I don't think Alessandro used Amber for energies, and if it's a simple program
> it probably is non-periodic. I think it's likely the 1-4 scaling factor for vdw.
> one of them ( can't recall, Adrian may know) either ele or vdw has the
> wrong 1-4 scaling in NAMD for amber ff.
> On Sat, Jul 26, 2008 at 8:36 PM, David A. Case <> wrote:
>> On Sat, Jul 26, 2008, Alessandro Nascimento wrote:
>>> I wrote a simple program to read some information in the prmtop file
>>> and compute nonbonded energies (ele+vdw) from a sander/pmemd
>>> trajectory and I am trying now to compare my first test results with
>>> the ones from the plugin NAMDEnergy in VMD. For electrostatic
>>> computation, they match perfectly. For vdw, however, seems like
>>> vmd/namd overestimates the energetic contribution. Does anyone has any
>>> experience on comparing results between amber and vmd/namd ?
>> I don't have experience, but as a guess: Amber by default includes a
>> correction for vdw interactions beyond the cutoff; NAMD might not inlcude
>> such a term. How different are the results?
>> ...dac
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> --
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> Carlos L. Simmerling, Ph.D.
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Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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