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

From: Semorale (semorale_at_gmail.com)
Date: Thu Aug 14 2008 - 12:26:58 CDT

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>

> 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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