Hi Francesco,
> The Giambasu-Case directions - albeit restricted to cpu only - seemed
> to invite to talk with amber, too. Sorry for the intrusion following
> my misunderstanding.
It's not an intrusion. I think you might have more chance of success on the NAMD forums. Especially if your topology and coordinate files match and work in VMD and the CPU version of NAMD. Then it might be something subtle going wrong inside the code and you might need an expert in the code to look at it.
> I'll do. I assumed that the files provided with the tutorial are
> correct. On the other hand, they load correctly to VMD. Better, I'll
Try just running on a single processor/single GPU - it might be an issue with multi GPU NAMD. Also see if VMD offers you any error messages in the console box when loading the files. I think the key will be to see if it works in the cpu version. You can download a binary of namd and just quickly try it with the single cpu version and see if that works. That will quickly tell you if it is the input files or a bug in the code.
> run myself xleap for a rectangular box. Curiously, xleap is not in my
> installation of amber11/ambertools1.5, while it is in the installation
> of amber10.
This sounds like it got skipped during installation because an X11 development library was missing. Did you compile the amber10 version on a different machine? - You could try running '$AMBERHOME/AmberTools/src/configure gnu' and see if it mentions anything about skipping the building of xleap. Normally this is because xorg-X11-devel (or similar) is not installed.
> > On another note why not just use GPU AMBER (PMEMD)?
>
> Present status of the Country, with drastic budgetary cuts, have
> forced us to priorities. I still am at amber10/ambertools1.5. More
> importantly, what i want to simulate can't be done with current
> amber11.
Fee waivers are available in circumstances where people do not have the funds to purchase a license. You can make a request to amber-admin.biomaps.rutgers.edu
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Received on Thu Oct 20 2011 - 01:30:04 PDT
