<br><br><div class="gmail_quote">2012/2/10 Tomáš Trnka <span dir="ltr"><<a href="mailto:ttrnka@mail.muni.cz">ttrnka@mail.muni.cz</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello all GMX devs,<br>
<br>
I've implemented the ASPC method for polarizable molecular dynamics (KOLAFA,<br>
J.; J. Comput. Chem. 2004, 25, 335-342) for GROMACS and would love to see this<br>
included in mainline.<br>
<br>
A simple benchmark with 216 SWM4-NDP water molecules shows that using ASPC the<br>
simulation is six times faster with energy drift reduced about fourfold<br>
compared to the steepest descent minimization.<br></blockquote><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
However, I've never used gerrit before and therefore would like to ask some<br>
questions first instead of going ahead blindly and making a mess:<br>
<br>
1) Is there any way to submit a patch series for review or do I have to squash<br>
it all into a single patch? (the GROMACS website keeps talking about a single<br>
commit everywhere in the Gerrit introduction AFAICS)<br></blockquote><div>Depends on the size of your commit (<1000 lines it is OK to have 1 commit - above it might be nicer to have more but not mandatory) and whether you can split it into more than one logical commit (each logical commit should add a new feature (or prepare something) and should be working correctly by itself). You don't want to commit the originally history with all the little fixup commits.</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2) Most of my changes are in the shellfc.c file and the coding style there<br>
doesn't match the guidelines at all (indent is two spaces, ifs/fors have<br>
braces on the same line) - shall I go for compliance with guidelines or<br>
consistency with the existing code?<br></blockquote><div>Either way is OK as long as it is somewhat consistent within your change. We will be fixing the formatting soon: <a href="http://redmine.gromacs.org/issues/845">http://redmine.gromacs.org/issues/845</a></div>
<div><br></div><div>Roland</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks for your time answering this.<br>
Best regards<br>
<br>
Tomáš Trnka<br>
<span class="HOEnZb"><font color="#888888">--<br>
Laboratory of Computational Chemistry<br>
National Centre for Biomolecular Research, Masaryk University<br>
Brno, Czech Republic<br>
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