Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Fri Jul 11 20:08:00 CEST 2003
Of course, it may be a periodic boundary effect. But then what would I do?
Should I remarkably increase the box-size accomodating much more water molecules and repeating the procedure?
From: David [mailto:spoel at xray.bmc.uu.se]
Sent: Fri 7/11/2003 2:03 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] helices
On Fri, 2003-07-11 at 19:44, Nagy, Peter I. wrote:
> Dear Gromacs Users!
> I performed a test run for two close, nearly parallel alpha helices
> 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
> 100 limit. Reading the recent mails on this list, I was not worried. I
> 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
> the Sybyl package, as well. The system in this case consisted of about
> water molecules + the dimer. I used periodic boundary, TIP3P water
> and allowd 1000 steps with the conjugate gradient method. Although the
> 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?
Simplest suggestion first: isn't it a periodic boundary effect? Energy
minimization will not move atoms more than a fraction of an Ångström.
> Peter Nagy
> Dept. Medicinal and Biological Chemistry
> The University of Toledo
> Toledo, OH 43606 USA
pnagy at utnet.utoledo.edu
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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