Re: namd energy

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Feb 05 2008 - 06:40:09 CST

Hi Leandro,
please have a look at
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node24.html#section:electdesc
to see how electrostatic switching actually works. Changing the value of
the switching distance and cutoff *will* alter your electrostatic energy
unless you're using PME. Also, while this isn't responsible for your
problem, I don't recommend using a switching distance and cutoff that
are the same, as it makes switching sort of useless (since the whole
point of switching is to avoid discontinuities in the vdw energy).
Best,
Peter

Leandro Martínez wrote:
>
> I'm trying to analyze some non-bonded energy terms with NAMD energy.
> I don't understand exactly the cause of some differences in the outputs.
> I'm computing the non-bonded interaction energies between two atoms,
> in one frame, for instance
>
> selection 1: index 1455
> selection 2: index 44
>
> The atoms, in this frame (the only one in my tests), are 2.2 angstroms
> appart.
>
> If use the NAMD energ plugin to compute their non-bonded interaction
> energies,
> I get different results, depending on the cutoff I use. For example:
>
> *
> cutoff 5 angs:*
> Frame Time Elec VdW Nonbond
> Total
> 0 0 -183.093 +21.1309 -161.962
> -161.962
> *
> cutoff 10 angs:*
> Frame Time Elec VdW Nonbond
> Total
> 0 0 -236.93 +21.1309 -215.799
> -215.799
> *
> cutoff 15 angs:*
> Frame Time Elec VdW Nonbond
> Total
> 0 0 -247.661 +21.1309 -226.53
> -226.53
> *
> cutoff: 100 Angs *
> Frame Time Elec VdW Nonbond
> Total
> 0 0 -260.94 +21.1309 -239.809
> -239.809
>
> The switch distance is always equal to the cutoff.
>
> If I try to compute the energy myself, using the distance and the
> force-field
> parameters, I get:
>
> Elec: -256.39
> VdW: +21.11
> Total: -235.28
>
> So I have two problems: one is that the electrostatic energy changes if
> one changes the cutoff in the range 5 to 100 angs, even while the
> atoms are 2.2 angs appart. The other is that I don't get exactly the same
> value for the VdW energy if I do the calculation myself, although these
> values are coherent to each other in the NAMD calculations.
> The system has periodic boundary conditions of about 80 angs, so I don't
> see how by changing the cutoff between 5 and 10 angs the result changes.
>
> Any help will be appreciated,
> Leandro.
>
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