VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Tue Mar 11 2008 - 20:05:46 CDT

Thank you both very much for providing solutions. :) I will have a look at
both of them.

Cheers,
Poker.

Quoting Peter Freddolino <petefred_at_ks.uiuc.edu>:

> This email seems particularly timely since it's the second that I've
> received in the last couple days about the switching issue. When I
> started working on namdenergy I'd assumed that people would mostly use
> it with PME, as with normal simulations. Since that doesn't seem to be
> the case, let me point out the following: The right way to deal with the
> cutoff dependence of electrostatic interactions without PME (which is
> due to switching) is to turn switching off, *not* to use very large
> cutoffs. I've committed a version of namdenergy to cvs that turns
> switching off if you feed it a switch distance that is blank (literally
> "", not just unspecified) or less than 0. The docs have been changed to
> reflect this. For now I've posted this version at
> www.ks.uiuc.edu/~petefred/namdenergy.tcl; it will be included in future
> vmd releases.
>
> Best,
> Peter
>
> poker_at_physics.usyd.edu.au wrote:
> > There's been an earlier thread (IIRC,) about interaction energy
> depending
> > on cutoff values used, but..
> >
> > I'm writing to ask whether people have a version of namdenergy.tcl (or
> > another script,) to calculate full electrostatics for a trajectory
> file at
> > each frame in a trajectory.
> > --
> > - What I have been doing so far is to set the cutoff at arbitrary
> large
> > values (say 5000 Angs., ), which gives a small difference of ~unit
> > kcal/mol for electrostatics. It's good enough, but really inelegant.
> > - There is a significant difference between cutoffs and full
> > electrostatics:
> > Cutoff(Angs.) Electrostatic (kcal)
> > 100 -239.163
> > 140 -224.893
> > 200 -215.19
> > 5000 -204.5
> > Quick script -205.38 (partially due to differences in accuracy
> constants
> > used?)
> > - We wish to compare energy calculations from NAMD simulation results
> with
> > its components, e.g. vacuum electrostatic potential, VdW, etc.
> >
> >
> > So, before making a customised version of the plug-in, I'm wondering
> if
> > this has been done already?
> >
> > ----------------------------------------------------------------
> > This message was sent using IMP, the Internet Messaging Program.
> >
>
=============
Quoting Leandro Martínez <leandromartinez98_at_gmail.com>:

> Hi, I have a fortran package that does that. It is the energy
> program that you can get from: http://lm-mdanalysis.googlecode.com
> There is a input file there that is quite self-explicative. Furthermore
> you need to create a pdb file containing "1.00" in the in the b-factor
> field for one of the groups of interest and "2.00" in the b-factor field
> for the other group. This package works only for non-bonded interactions.
>
> Don't use namd-energy with large cutoffs, the results are wrong because
> of some problems in the namd pairlist option. The way of doing
> this with namdenergy is turnning the switching off.
>
> Leandro.

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