[gmx-users] 3.2.1 vs 3.3

David Mobley dmobley at gmail.com
Wed Jan 4 20:38:18 CET 2006

One thing I did initially was to use mdrun -rerun to actually reprocess some
of my 3.2 trajectories in 3.3 and make sure the energies I got still made
sense. They did. Of course, you have to do that _after_ installing 3.3. You
can presumably do other tests if you want, but it may take some thought to
decide what the best tests are. Also, there are numerous bugfixes
implemented in 3.3, so it is possible that you may get different answers
with 3.3 if you are computing something that's affected  by a bugfix. Also,
there was a bugfix to mdrun -rerun at some point (I forget whether it was
before or after 3.3) so if you use the mdrun -rerun option to compare, you
will want to make sure you are using the bugfix.

Others may have thought more carefully about this than I have. I didn't look
for exact agreement since I was doing free energy calculations and there
were some bugfixes which applied to these, but I made sure reprocessed
trajectories had energies and dv/dlambdas consistent with what I expected.
Generally, my advice in any version of GROMACS or any other package is to
begin by calculating something where the right answer is known, and make
sure you get the right answer. :)

David Mobley
Dill group

On 1/4/06, Jon <jon.ellis at utoronto.ca> wrote:
> Hello I've been using gromacs for about a year and have performed a
> number of simulations on version 3.2.1.
> I would like to upgrade to 3.3. This may seem like a silly question, and
> I apologize if its been discussed in the list before, but before I
> install 3.3, can I compare results seemlessly between my old 3.2 runs
> and any new runs on 3.3?
> Thanks
> for your help
> Jon
> --
> ----------
> Jon Ellis
> PhD Candidate, Thompson Group
> Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
> University of Toronto
> LM147 - (416) 978-6568
> jon.ellis at utoronto.ca
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