[gmx-users] helices
David
spoel at xray.bmc.uu.se
Fri Jul 11 21:17:01 CEST 2003
On Fri, 2003-07-11 at 20:39, Nagy, Peter I. wrote:
> Dear David!
> 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
Forget about the water! To test whether you have a PBC problem, you
don't need any water.
Now, if your molecule is elongated (as it probably is) you can use
editconf -princ to align it along the principal components, i.e. the
long axis. You could the use a rectangular box and save on the amount of
water, however there is a possibility that in a simulation the molecule
will rotate by 90 degrees and interact with itself, which you don't want
in general.
> 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?
>
> Peter Nagy
>
>
> -----Original Message-----
> From: David [mailto:spoel at xray.bmc.uu.se]
> Sent: Fri 7/11/2003 2:15 PM
> To: gmx-users at gromacs.org
> Cc:
> 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
> > Cc:
> > 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
> > > 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?
> > 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
> > http://xray.bmc.uu.se/~spoel
> >
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> >
> --
> 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
> http://xray.bmc.uu.se/~spoel
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>
--
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 http://xray.bmc.uu.se/~spoel
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