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. <br>
<br>
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. :)<br>
<br>
David Mobley<br>
Dill group <br>
UCSF<br>
<br><br><div><span class="gmail_quote">On 1/4/06, <b class="gmail_sendername">Jon</b> <<a href="mailto:jon.ellis@utoronto.ca">jon.ellis@utoronto.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello I've been using gromacs for about a year and have performed a<br>number of simulations on version 3.2.1.<br><br>I would like to upgrade to 3.3. This may seem like a silly question, and<br>I apologize if its been discussed in the list before, but before I
<br>install 3.3, can I compare results seemlessly between my old 3.2 runs<br>and any new runs on 3.3?<br><br>Thanks<br>for your help<br>Jon<br><br><br><br>--<br>----------<br>Jon Ellis<br>PhD Candidate, Thompson Group<br>
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry<br>University of Toronto<br>LM147 - (416) 978-6568<br><a href="mailto:jon.ellis@utoronto.ca">jon.ellis@utoronto.ca</a><br>_______________________________________________
<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br>