Re: dummy atom mass changed

From: yun luo (luoyun724_at_gmail.com)
Date: Mon May 04 2009 - 16:24:59 CDT

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:

> Ly,
>
> 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
> NAMD2.7b1.
>
> NAMD2.6 FEP tutorial:
> http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.pdf
>
> Required files for tutorial:
> http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.zip
>
>
> C.
>
>
> --
> 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 <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
>
> On Mon, May 4, 2009 at 2:54 PM, yun luo <luoyun724_at_gmail.com> wrote:
>
>> Hi,
>>
>> 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?
>>
>> Thanks!
>>
>> Ly
>>
>
>

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