[gmx-developers] Coming on to help in GROMACS development

Erik Lindahl lindahl at sbc.su.se
Tue Mar 15 16:38:14 CET 2005


The only major outstanding part for 3.3 is the QM/MM interface, and 
then there's some minor clean-up and testing.  I'd suggest waiting 
until after that release before we add significant new functionality.

David recently suggested that we should fork off the 3.3-release branch 
so new stuff could be added in the head, but that only works if 
somebody volunteers to do all the boring testing in the separate 
release branch, so I'd rather force ourselves to fix it by freezing 
head until we get it done...



On Mar 15, 2005, at 3:40 PM, Michael Shirts wrote:

> Before I head into the response, one thing I wanted to check is what
> the release schedule is for the next versions of GROMACS, so I will
> know how to time my contributions.  It's been hard to get any
> information out on this subject :)
> Back to the response:
>> This depends a lot on the system I guess.
>> For many system you do want to turn of the intramolecular non-bonded
>> terms as the ensemble of the molecule would become very different
>> in the vapor state, whereas a molecule without non-bonded interactions
>> might have an ensemble closer to the solvated state.
> Right, so this should be a configurable option.
>> I guess that in put_in_list you would just have to check if both atoms
>> are perturbed instead of only one in the pair.
>> I have also made some changes put_in_list, especially for free-energy
>> simulations
> Yep, that's pretty much what needs to be done.
>> I accidentally put a question mark at the last line.
>> I meant that I have implemented this and that it is in CVS.
> Very good, I'll look over it.
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