[gmx-users] Testing (was: Tyrosine problems again)

[David van der Spoel]

dichan at ucalgary.ca wrote:
> Hello once again
> 
> As per the suggestions, I went ahead and installed an older version of the
> gcc compiler: version 3.4.
> 
> I then re-installed fftw and gromacs3.3.3 using the following commands:
> 
> ./configure --enable-float --enable-threads --enable-sse
> --prefix=/home/david/fftw-gcc3 CC=/usr/lib64/ccache/gcc34
> CXX=/usr/lib64/ccache/g++34
> 
> ./configure LDFLAGS=-L/home/david/fftw-gcc3/lib
> CPPFLAGS=-I/home/david/fftw-gcc3/include
> --prefix=/usr/local/gromacs-single-3.3.3-gcc3 CC=/usr/lib64/ccache/gcc34
> CXX=/usr/lib64/ccache/g++34
> 
> The compilation seems to finish, but I do still find a couple of error
> instances:
> 
> conftest.c: In function `main':
> conftest.c:42: error: `not' undeclared (first use in this function)
> conftest.c:42: error: (Each undeclared identifier is reported only once
> conftest.c:42: error: for each function it appears in.)
> conftest.c:42: error: syntax error before "big"
> 
> conftest.c: In function `main':
> conftest.c:51: error: void value not ignored as it ought to be
> 
> Wno-unused -funroll-all-loops -I/home/david/fftw-gcc3/include conftest.c >&5
> conftest.c:74: error: syntax error before "ac__type_new_"
> conftest.c:74: warning: type defaults to `int' in declaration of
> `ac__type_new_'
> conftest.c:74: warning: data definition has no type or storage class
> conftest.c: In function `main':
> conftest.c:86: error: syntax error before ')' token
> 
> Do these indicate my configure run failed? Sorry, I just don't know what
> to make of these.
> 
> Gromacs runs after, but I am still getting odd tyrosine behaviour. The
> dihedral once again resembles a chair at the beginning and then settles
> down during extended equilibration. Based on previous experience I am not
> used to this sort of behaviour - can anyone confirm this is something to
> worry about? (www.ucalgary.ca/~dichan/gcc3_h2o_eq.jpg)
> 
> Cheers,
> 
> David

Do you use pressure coupling? If so, what time constant?
As I said previously, we recently had problems on ring systems with 
tau_P = 1 ps, with tau_P = 5 ps it was fine. The fluctuations of the box 
size coupled to the forces on the ring substituents.

> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se