[gmx-users] Tyrosine problems again

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 31 21:19:08 CEST 2008

dichan at ucalgary.ca wrote:
> Hi everyone
> I am having trouble (again) with my tyrosine residue. For some reason
> during early steps of my simulation, the ring of the tyrosine residue does
> not remain planar but rather is distorted - enough at times to look like a
> chair conformation. Earlier I thought this was a vsite=aromatics issue
> only, but I am now using vsite=hydrogens (ffG43a2 and gromacs3.3.3) and
> I'm still getting odd data. I thought it might be installation related
> since I got a new machine (quad core, FC9, x86_64) and as such, I
> reinstalled:
> In fftw-3.1.2
> ./configure --enable-float --enable-threads --enable-sse
> --prefix=/home/david/fftw
> make
> make install
> In gromacs3.3.3:
> ./configure LDFLAGS=-L/home/david/fftw/lib
> CPPFLAGS=-I/home/david/fftw/include
> --prefix=/usr/local/gromacs-single-3.3.3
> make
> make install
> These procedures are based on the gromacs installation guide - am I
> missing anything for my specific setup/architecture? I'm not too familiar
> with all the options but think I got it right.
> Although the EM now looks fine, during the first 70 steps of position
> restrained equilibration the tyrosine still buckles a lot (e.g. dihedral
> angle of > 70 degrees in the ring although it should be ~0) and settles
> down after about 70 steps (http://ucalgary.ca/~dichan/multiplot.jpg).
> Any suggestions are very appreciated!!!
> Thanks!
> David
> P.S. Another symptom is that at times when I run the same tpr file I get
> different outcomes. I use the same cpu, simply cp 1.tpr 2.tpr and run
> 2.tpr and the outcome is different from the first. When I run diff on the
> tprs or gmxcheck, it tells me the two files are the same. I know this
> shouldn't happen, but...

this sounds A LOT like a compiler problem..
which gcc do you use?

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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

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