From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon May 04 2009 - 17:39:22 CDT
As you said, the only reason why the dummy atom is needed is because
NAMD 2.6 does not have soft-core potentials. The purpose of the
tutorial is somewhat academic, in that the "charging free energy" is
only meaningful within some theories of ion solvation, and is not an
If you want a complete solvation free energy, then it is not necessary
to follow the tutorial's "pseudo-single topology" approach.
Note that if for some reason, you do want to use a dummy atom, its
mass will not affect the thermodynamics of the system. It should
typically not be less than 1.0, otherwise you may need to use smaller
timesteps to preserve the stability of the simulation.
One more remark: even the charging free energy can now be computed
without the help of a dummy atom, since NAMD 2.7b1 allows for the
separate decoupling of electrostatic and L-J interactions, through the
fepElecLambdaStart and fepVdwLambdaEnd parameters.
On Mon, May 4, 2009 at 5:24 PM, yun luo <luoyun724_at_gmail.com> wrote:
> Hi Chris,
> Thank you for your reply.
> Actually, I did follow the FEP tutorial part 2. Charging a spherical ion
> using dual-topology paradigm. That's why I want add a dummy atom. In the
> tutorial one adds a dummy atom with 0 charge but the same radius as sodium
> because there is no soft-core contribution in NAMD2.6. Since NAMD2.7 has
> soft-core part, I think I need using a dummy atom with 0 charge 0 radius to
> get both elec and vdW energy. But do you think the a dummy atom with nonzero
> mass will cause problem?
> Many thanks!
> On Mon, May 4, 2009 at 3:33 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
>> With 0 charge, 0 mass, and 0 radius the dummy particle is effectively the
>> same as no atom .... which is of course the desired effect usually.
>> Assuming you're not doing something unusual, then you don't need the dummy
>> particle. You should be able to just make the Na disappear.
>> The FEP tutorial may be of help in setting up calculations. This tutorial
>> is for NAMD 2.6 but the system setup process should be the same as
>> NAMD2.6 FEP tutorial:
>> Required files for tutorial:
>> Chris Harrison, Ph.D.
>> Theoretical and Computational Biophysics Group
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>> char_at_ks.uiuc.edu Voice: 217-244-1733
>> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>> On Mon, May 4, 2009 at 2:54 PM, yun luo <luoyun724_at_gmail.com> wrote:
>>> I'm using NAMD2.7 for running FEP. I need to disappear a sodium ion in my
>>> membrane. So I overlay a dummy atom with 0 mass 0 charge 0 radius on a
>>> sodium ion. But I got a warning below:
>>> Warning: FOUND 1 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO 0.001
>>> I'm wondering if the nonzero mass will effect the energy? If yes, how to
>>> stop this automatic changing?
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