On Mon, Mar 11, 2013 at 6:34 PM, David Winogradoff <dwino218.gmail.com>wrote:
> I am currently working on a project using amber in parallel to conduct
> a long REMD run. A few weeks ago, using the same input file that
> worked before (modified to start from where the previous simulation
> ended), my parallel run failed with a generic openmpi error message.
> After some initial hesitation, I decided to delete my installation of
> amber 12 and recompile and rebuild. I have run 'make test'
> successfully with my new serial and parallel versions of amber 12, but
> my REMD simulation still won't run. After many unsuccessful attempts
> to run, I decided to look at some of my previous output files. To my
> surprise, the older output files had amber 11 at the top. Even though
> my new simulations won't run, they do write the header, which says
> amber 12.
>
> I did see that it is possible to have some combination of amber 11 and
> amber 12, but I never installed amber 11 and do not have the tar files
> to do so. Is there any way to install amber 11 with amber 12 tar files
> (accidentally)? My hypothesis is that some requirement, such as my
> version of gnu, was out of date during my previous installation,
> preventing the complete installation of amber 12. I have tried to
> recreate the mistake, since I didn't think I could make files meant
> for amber 11 to work with amber 12, without success. The only solution
> I can think of right now is to purchase amber 11 and create a hybrid
> form of amber 11 and amber 12 that will hopefully run my simulations
> once more.
>
When Amber 12 was released, it actually still said "Amber 11" at the top.
That was updated in bugfix.2 for Amber 12. Do you have all bug fixes
applied?
What error messages are you getting? And what exactly are you doing? The
better way forward, IMO, is to fix Amber 12... What kind of REMD are you
doing?
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 11 2013 - 16:00:03 PDT
