[gmx-users] helices

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Fri Jul 11 19:46:01 CEST 2003

Dear Gromacs Users!

   I performed a test run for two close, nearly parallel alpha helices with 
26+26+NAC+ACE residues. The net charge of the system was just zero because of having only one ASP and one LYS residues. The helices were slightly shifted with respect to each other, and the header of the second helix was at a height of 1/3 total length of the first one (so 2/3 of both helices were close and parallel). The system was solvated by 620 SPC waters. 
   In performing the energy minimization, I used the steepes descent method, setting rlist, rcoulomb, and rvdw to 0.9 (nm). 
   Minimization stopped at 780 out of 1000 steps but did not reach the emtol=
100 limit. Reading the recent mails on this list, I was not worried. I started
a 200 ps MD run, and checked the .xtc trajectory in ngmx.
   Ngmx starts displaying structures at t=0 ps, thus with the structure obtained as the output of the energy minimization. This is, at least, that I
presumed. Then I was very much surprised that the structure at that point was
close to a collinear pair of two alpha helices. I understood it that this structure was created by the energy minimization.
   I performed an energy minimization of the original dimer structure using 
the Sybyl package, as well. The system in this case consisted of about 1500
water molecules + the dimer. I used periodic boundary, TIP3P water molecules
and allowd 1000 steps with the conjugate gradient method. Although the two
energy minizmizations differ in some technical elements, but it does not explain for me the result: the dimer structure was pactically unchanged in 
Sybyl after 1000 steps. 
   Then why did the GROMACS energy minimizer change (if it really changed, as I suspect) the relative positions of the two helices?

Peter Nagy
Dept. Medicinal and Biological Chemistry
The University of Toledo
Toledo, OH 43606 USA
pnagy at utnet.utoledo.edu
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