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... _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
