From: Ana Celia Araujo Vila Verde (
Date: Sat Dec 17 2005 - 14:23:01 CST



My name is Ana and I'm a post-doc at Penn State University, and I'm a new user of NAMD. I've been using the tutorial to get started and found it in general very clearly written and extremely useful. I was also at the Beckman institute group for a couple of weeks just recently so I could benefit from hands-on experience there, which was wonderful.


While talking to Elizabeth Villa and others we found that there is a part of the tutorial that could be improved.

1) It would be very useful if you could provide a model configuration file, for example taking the ubiquitin in a water box or in a water sphere examples, of restart analyses. Since restart analyses configuration files are very different from the initial files, it would save new users a lot of time if you could provide a commented template for a restart file.

2) Explaining what PMEGridSizeX ( or PMEGridSizeY or PMEGridSizeZ) is would benefit from a more detailed text and also from an example. Something like this is what I had in mind:

For PMEGridSizeX, one should use a number as close as possible (can be a bit bigger or smaller) to the number on cellBasisVector1, but one that can also be factorized in 2's, 3's or 5's (the smaller the better). This will great a grid in which each grid point is 1 angstrom apart from the next, and will make the Fast Fourier Transforms that exist in this part of the code much faster. A similar thing should be done for PMEGridSizeY and PMEGridSizeZ. Here's an example: if the cellBasisVector1 is (63,0,0) then a good PMEGridSizeX would be 64 because 64=26. 60 is less good because 60=2*2*3*5.


I hope this is helpful to you. All the best,






Ana CÚlia Ara˙jo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802



Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846



** Visit for more info on majordomo