[gmx-users] 3.2.1 vs 3.3

Jon Ellis jon.ellis at utoronto.ca
Thu Jan 5 06:04:08 CET 2006

Thanks for your help, David. Sound advice. I don't want to rerun my full 
trajectories, as this can take quite a while, but I will try to run some 
shorter simulations on my system to compare. 

I am not rigidly concerned with reproducing the EXACT results, so as long as 
they are consistent.

I will keep the mailing list updated as to what I find.


> On 1/4/06, David Mobley <dmobley at gmail.com > wrote:
> 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
Ph.D. Candidate
Institute of Biomaterials and Biomedical Engineering/Department of Chemistry
University of Toronto
ph. (416) 978-6568
email. jon.ellis at utoronto.ca

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