From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 06 2011 - 16:39:41 CDT

Hi,

On Wed, Apr 06, 2011 at 05:30:45PM -0400, Raul Araya wrote:
> Dear John
>
> Thanks very much for your answer.
>
> A small question regarding the "coulombmsm"? Do you think is better to use
> that tool instead of PMEpot?

If you don't have a good CUDA-capable GPU, then PMEPot is probably faster,
but it is just giving you the long-range part of the field, and it
doesn't handle partially- or non-periodic systems.

> An a second one, when calculating "coulombmsm" the calculation must be
> done over all atoms, as when one uses PMEpot??

No, with both PMEPot and the CoulombMSM you can use any atom selection
you want and only those atoms will contribute to the potential map...
See Extensions->Analysis->PMEPot and Extensions->Analysis->VolMap Tool.
The "selection" field in both tools is how you tell them which atoms
are contributing to the potential map.

The main thing is that you must have partial charges assigned to your
structure, so make sure to load a PSF file or similar when you load your
model into VMD. You will end up without charges if you just
load a PDB file by itself...

When it comes time to make your figures, set the "color scale data range"
controls in the "Trajectory" tab of the graphical representations window.
A good range for potential maps is often -10 to 10.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

>
> Thx again-
>
> Raul Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Fisicas y Matematicas.
> Universidad de Chile.
>
> 2011/4/6 John Stone <johns_at_ks.uiuc.edu>
>
> Hi,
> The oldest papers did these calculations inside a modified version
> of NAMD. Subsequent to that, we added the "PMEPot" plugin to VMD, which
> can do time averaging, but only for the frames that you've got loaded
> in memory in VMD (e.g. not via bigDCD). There is now also a new volmap
> command that computes electrostatic fields, and this is used by the
> VolMap plugin (a GUI front-end for these commands). The volmap
> "coulombmsm" electrostatics mode is more flexible than the PMEPot
> as it handles periodic, partially periodic, and non-periodic systems,
> it incorporates both the short-range and long-range potentials,
> and it can use GPUs to speed up the calculation by up to 20-40x
> (for a fast GPU). As with PMEPot, the volmap potential time-averaged
> calculations also work only with frames that are loaded into memory,
> so they won't work with BigDCD. In the short-term, you could either
> do your time-averaged calculations on a subset of frames, or average
> groups of frames at a time, and then average the averages...
> In the long-term, VMD will enable you to work with unlimited size
> trajectory files without having to use the BigDCD script anymore, but
> I can't give you a firm timeline for that feature yet.
>
> In terms of visualization, one can either use the built-in
> VolumeSlice representation and an appropriate choices of color
> scale and color scale data range settings, or you can load the
> resulting potential map in to OpenDX, AVS, Matlab, or some other
> tool and render the contour map separately and photoshop it into
> your image. I find it more convenient to use the VolumeSlice
> representation that is built into VMD, and just write a script to
> set a custom-designed color scale that gives the contoured look
> one gets in tools like Matlab.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 06, 2011 at 02:13:58PM -0400, Raul Araya wrote:
> > Dear VMD users:
> >
> > Im interested in rendering electrostatic potential maps such as
> those
> > described in : "Imaging alpha-hemolysin with molecular dynamics:
> Ionic
> > conductance, osmotic permeability and the electrostatic potential
> map".
> > Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal,
> 88:3745-3761,
> > 2005, and other papers. My questions regarding the generation of
> such maps
> > are:
> >
> > 1) They make use of the PMEpot plugin, but is there a way to use it
> with
> > bigdcd i order to get an average of al frames in a MD?
> >
> > 2) In the mentioned paper the authors comment that the average is
> done
> > over the MD and also over the "sevenfold symmetry of a-hemolysin",
> how
> > does this averaging is made? In my case I'm working with an
> hexameric
> > trans-membrane channel protein.
> >
> > 3) and this is a very technical question: How do you get from one
> 3d .dx
> > potential map to the 2d contour maps depicted in the mentioned
> paper (an
> > in others) ??
> >
> > Thanks.
> >
> > Raul Araya Secchi
> > B.Sc Molecular Biotechnology.
> > Molecular Biotechnology Engineer.
> > PhD Student (Biotechnology Program. UNAB, Chile)
> > Computational Biology Lab (DLab)
> > Center for Mathematical Modeling (CMM)
> > Facultad de Ciencias Fisicas y Matematicas.
> > Universidad de Chile.
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078