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<p class=MsoNormal>Dear Gromacs-Developers – <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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.<o:p></o:p></p>
<p class=MsoNormal>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 hurt.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks so much,<o:p></o:p></p>
<p class=MsoNormal>Looking forward to communicating with you,<o:p></o:p></p>
<p class=MsoNormal>Nick Schafer<o:p></o:p></p>
<p class=MsoNormal><a
href="http://sbel.wisc.edu/People/schafer/mainframeset.html">http://sbel.wisc.edu/People/schafer/mainframeset.html</a><o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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