Re: Problems with TMD could not be solved with the CVS version

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 15 2008 - 07:51:45 CDT

Hi Samuel,
the CVS version should have TMD working properly, to my knowledge (with
the possible exception of the TMD/tclforces combination mentioned by
Gianluca).
Peter

Semorale wrote:
> Hi All !!
>
> Peter, that we use charmm 6.0, ensures that TMD work properly in the
> CVS version (using multiple processes), that is, effectively
> diminishing the RMSD to zero?
>
> Thanks and greetings to all
>
> SAMUEL
>
> 2008/8/14 Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>>
>
> Hi Robert,
> it's difficult to offer any useful suggestions without knowing
> what error message you received. However, I would point out that
> if you're building the recent cvs versions of namd you should be
> building against charm 6.0, not 5.9.
>
> Best,
> Peter
>
>
> Robert Schulz wrote:
>
> Hello everybody,
> I have been trying to get TMD running for quite some time. But
> the problem is, as already discussed in former threads, the
> rmsd increases.
> Interestingly, this appears to be only a problem for
> computations running on multiple CPU cores. For example, the
> unfolding of an helix works properly, as long as I run the TMD
> on one CPU core, but virtually breaks apart when using
> multiple processes.
> Unfortunately, I cannot use TMD with my system of interest in
> a single-core run due to the system size.
>
> Are there any updates considering this problem, for example in
> the CVS version? In one thread, it was believed to be so,
> which appears
>
> Currently, I was trying to compile this version on our Linux
> cluster, but got some strange syntax error messages, with both
> gnu compiler and pathscale. I was following the instructions from
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
> using tcl8.4.19, fftw-2.1.5, charm 5.9 and the net-linux-amd64
> option.
>
> Any suggestions are pretty welcome.
> Thanks in advance.
>
> Regards,
>
> Robert Schulz
>
>
>

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