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

John D. Chodera jchodera at gmail.com
Wed Jun 27 00:02:50 CEST 2007

Hi Nick,

If your primary interest is investigating new integration algorithms,  
you will definitely want to check out ProtoMol, a modular, open- 
source C++ code intended primarily for allowing rapid prototyping and  
testing of new MD integrators.  It will be much, much easier for you  
to work with than gromacs for this purpose:


Jesus Izaguirre, from Notre Dame, has written a number of papers on  
new integrators using this code:


Good luck,

- John

Dr. John D. Chodera <jchodera at gmail.com>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021

On Jun 25, 2007, at 1.59 PM, Nick Schafer wrote:

> 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 hurt.
> Thanks so much,
> Looking forward to communicating with you,
> Nick Schafer
> http://sbel.wisc.edu/People/schafer/mainframeset.html
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