Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Fri Jul 11 20:40:02 CEST 2003
I assume that when you write "make it 10 times as big" you mean the total
volume. I increased the edges by a factor of 2.2-2.5, and resolvated the
sytem. More than 10,000 water were added that I think to be enormously too
many. With a smaller box I still got 5758 waters. I think it is still too many. In Sybyl cca 1500 were added. I try to find a box including about 3000
water molecules, I assume they would suffice? Do you agree?
From: David [mailto:spoel at xray.bmc.uu.se]
Sent: Fri 7/11/2003 2:15 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] helices
On Fri, 2003-07-11 at 20:06, Nagy, Peter I. wrote:
> Dear David!
> 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?
Just the box size will do for a test, just edit the last line in the gro
file, make it 10 times as big. mdrun will always keep the proteins in
the box, but the algorithm makes that proteins can easily jump. If it is
a pbc effect you box is definitely too small, unless this is a crystal.
Is it maybe the ice-binding protein?
> Peter Nagy
> -----Original Message-----
> 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
> > 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
> > 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
> > 2/3 of both helices were close and parallel). The system was
> > 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
> > emtol=
> > 100 limit. Reading the recent mails on this list, I was not worried.
> > 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
> > 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
> > using
> > the Sybyl package, as well. The system in this case consisted of
> > 1500
> > water molecules + the dimer. I used periodic boundary, TIP3P water
> > molecules
> > and allowd 1000 steps with the conjugate gradient method. Although
> > 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?
> 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
> Groeten, David.
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
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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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