[gmx-developers] Feasibility of implementing new integration schemes in Gromacs

Nick Schafer npschafer at wisc.edu
Mon Jun 25 22:59:58 CEST 2007

Dear Gromacs-Developers - 


First of all, I should point out that I am completely new to this list and
also quite new to MD in general.  My name is Nick Schafer and I am an
undergraduate student at the University of Wisconsin, Madison working for
Professor Dan Negrut in the mechanical engineering department.  I'm working
with Professor Negrut on testing new integration algorithms for molecular
dynamics.  After some deliberation and one or two false starts, we have
decided to attempt to modify NAMD-Lite (formerly MDX), a watered down,
sequential version of NAMD (a code that I assume you are all at least
familiar with by name).  So far it is going fairly well.  The documentation
for NAMD-Lite is fairly good and the code is understandable.  In the coming
months, I will (hopefully) be implementing our integrators, designing and
performing several experiments, and analyzing/writing up our results.

This is where GROMACS comes in.  I recently switched from Windows to Linux
as a development platform and I was browsing the "Science" section of the
Synaptic Package Manager and noticed GROMACS.  I decided to look into it and
I found your webpage and this e-mailing list.  My basic question is: Would
GROMACS be a good choice for testing new methods of integration?  Would it
be feasible for me to modify/recompile the code?  One reason I am interested
in GROMACS is that it doesn't have the biology bias that NAMD does, but I
could still use VMD to analyze the results of my experiments.  Does anyone
here know of any reason why I should attempt to modify one code or the
other?  Any help is appreciated and don't be afraid to point out anything
that I said that sounds crazy or is completely wrong.  My feelings won't be


Thanks so much,

Looking forward to communicating with you,

Nick Schafer



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