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<P><FONT SIZE=2>Dear David!<BR>
I assume that when you write "make it 10 times as big" you mean the total<BR>
volume. I increased the edges by a factor of 2.2-2.5, and resolvated the<BR>
sytem. More than 10,000 water were added that I think to be enormously too<BR>
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<BR>
water molecules, I assume they would suffice? Do you agree?<BR>
<BR>
Peter Nagy<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: David [<A HREF="mailto:spoel@xray.bmc.uu.se">mailto:spoel@xray.bmc.uu.se</A>]<BR>
Sent: Fri 7/11/2003 2:15 PM<BR>
To: gmx-users@gromacs.org<BR>
Cc: <BR>
Subject: RE: [gmx-users] helices<BR>
<BR>
On Fri, 2003-07-11 at 20:06, Nagy, Peter I. wrote:<BR>
> Dear David!<BR>
> Of course, it may be a periodic boundary effect. But then what<BR>
> would I do?<BR>
> Should I remarkably increase the box-size accomodating much more water<BR>
> molecules and repeating the procedure?<BR>
Just the box size will do for a test, just edit the last line in the gro<BR>
file, make it 10 times as big. mdrun will always keep the proteins in<BR>
the box, but the algorithm makes that proteins can easily jump. If it is<BR>
a pbc effect you box is definitely too small, unless this is a crystal.<BR>
Is it maybe the ice-binding protein?<BR>
<BR>
><BR>
> Peter Nagy<BR>
><BR>
><BR>
> -----Original Message-----<BR>
> From: David [<A HREF="mailto:spoel@xray.bmc.uu.se">mailto:spoel@xray.bmc.uu.se</A>]<BR>
> Sent: Fri 7/11/2003 2:03 PM<BR>
> To: gmx-users@gromacs.org<BR>
> Cc: <BR>
> Subject: Re: [gmx-users] helices<BR>
><BR>
> On Fri, 2003-07-11 at 19:44, Nagy, Peter I. wrote:<BR>
> > Dear Gromacs Users!<BR>
> ><BR>
> > I performed a test run for two close, nearly parallel alpha<BR>
> helices<BR>
> > with<BR>
> > 26+26+NAC+ACE residues. The net charge of the system was just zero<BR>
> > because of having only one ASP and one LYS residues. The helices<BR>
> were<BR>
> > slightly shifted with respect to each other, and the header of the<BR>
> > second helix was at a height of 1/3 total length of the first one<BR>
> (so<BR>
> > 2/3 of both helices were close and parallel). The system was<BR>
> solvated<BR>
> > by 620 SPC waters.<BR>
> > In performing the energy minimization, I used the steepes descent<BR>
> > method, setting rlist, rcoulomb, and rvdw to 0.9 (nm).<BR>
> > Minimization stopped at 780 out of 1000 steps but did not reach<BR>
> the<BR>
> > emtol=<BR>
> > 100 limit. Reading the recent mails on this list, I was not worried.<BR>
> I<BR>
> > started<BR>
> > a 200 ps MD run, and checked the .xtc trajectory in ngmx.<BR>
> > Ngmx starts displaying structures at t=0 ps, thus with the<BR>
> > structure obtained as the output of the energy minimization. This<BR>
> is,<BR>
> > at least, that I<BR>
> > presumed. Then I was very much surprised that the structure at that<BR>
> > point was<BR>
> > close to a collinear pair of two alpha helices. I understood it that<BR>
> > this structure was created by the energy minimization.<BR>
> > I performed an energy minimization of the original dimer<BR>
> structure<BR>
> > using<BR>
> > the Sybyl package, as well. The system in this case consisted of<BR>
> about<BR>
> > 1500<BR>
> > water molecules + the dimer. I used periodic boundary, TIP3P water<BR>
> > molecules<BR>
> > and allowd 1000 steps with the conjugate gradient method. Although<BR>
> the<BR>
> > two<BR>
> > energy minizmizations differ in some technical elements, but it does<BR>
> > not explain for me the result: the dimer structure was pactically<BR>
> > unchanged in<BR>
> > Sybyl after 1000 steps.<BR>
> > Then why did the GROMACS energy minimizer change (if it really<BR>
> > changed, as I suspect) the relative positions of the two helices?<BR>
> Simplest suggestion first: isn't it a periodic boundary effect? Energy<BR>
> minimization will not move atoms more than a fraction of an Ångström.<BR>
><BR>
><BR>
> ><BR>
> ><BR>
> > Peter Nagy<BR>
> > Dept. Medicinal and Biological Chemistry<BR>
> > The University of Toledo<BR>
> > Toledo, OH 43606 USA<BR>
> pnagy@utnet.utoledo.edu<BR>
> --<BR>
> Groeten, David.<BR>
> ________________________________________________________________________<BR>
> Dr. David van der Spoel, Dept. of Cell and Molecular Biology<BR>
> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
> phone: 46 18 471 4205 fax: 46 18 511 755<BR>
> spoel@xray.bmc.uu.se spoel@gromacs.org <BR>
> <A HREF="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</A><BR>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>
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><BR>
><BR>
--<BR>
Groeten, David.<BR>
________________________________________________________________________<BR>
Dr. David van der Spoel, Dept. of Cell and Molecular Biology<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</A><BR>
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