VMD-L Mailing List

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Wed Jun 08 2011 - 10:56:40 CDT

Hi John,

would you mind sharing the detailed description on the coulombmsm
option, for example, how to enable PBC and set up PME? It seems
coulombmsm is not covered in the User Guide. Some clarification is
greatly appreciated.

Regards,
Guanglei

On Wed, Apr 6, 2011 at 5:23 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> 

-- 
Guanglei Cui