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<TITLE>RE: [gmx-users] helices</TITLE>
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<P><FONT SIZE=2>Dear David!<BR>
Of course, it may be a periodic boundary effect. But then what would I do?<BR>
Should I remarkably increase the box-size accomodating much more water molecules and repeating the procedure?<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 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 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 (so<BR>
> 2/3 of both helices were close and parallel). The system was 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 the<BR>
> emtol=<BR>
> 100 limit. Reading the recent mails on this list, I was not worried. 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 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 structure<BR>
> using<BR>
> the Sybyl package, as well. The system in this case consisted of 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 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 <A HREF="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</A><BR>
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