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On 11/02/2012 2:48 AM, francesca vitalini wrote:
<blockquote
cite="mid:CAPRCF+Lvcad28ETLsrOWpdtiPxu+e6ff4n7wKnB+-sDh3-pJjw@mail.gmail.com"
type="cite">In fact in the reverse transformation I'm feeding the
CG structure information. <br>
</blockquote>
<br>
Yes, but you need a source of atomistic intra-residue knowledge
about protein structure in order to convert a CG structure to
something that is vaguely plausible at FG.<br>
<br>
<blockquote
cite="mid:CAPRCF+Lvcad28ETLsrOWpdtiPxu+e6ff4n7wKnB+-sDh3-pJjw@mail.gmail.com"
type="cite">Once I look through VMD to the FG structure I notice
that the backbones are not in planes so definitely I need to run
some minimization there. In the tutorial they were using
simulating annealing, but I don't think I need more than energy
minimization for that.<br>
What do you think?<br>
</blockquote>
<br>
So you've learned that any kind of simple restraint based on the
input FG structure is likely to produce a garbage result because the
atomistic detail of the input FG structure is garbage. Simulated
annealing does sound like a good way to start refining the
structure. You need something capable of more than local
minimization, unlike EM. Tiny time steps are probably necessary to
cope with the large forces.<br>
<br>
In GROMACS 4.5 you could use some COM virtual sites (or similar, see
manual) to have position restraints to the positions of the original
beads. If you feel the result of the above refinement has deviated
too much for whatever your real purpose is, then taking the refined
structure and introducing such v-site position restraints could be
useful.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPRCF+Lvcad28ETLsrOWpdtiPxu+e6ff4n7wKnB+-sDh3-pJjw@mail.gmail.com"
type="cite"><br>
<br>
<br>
<div class="gmail_quote">2012/2/10 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>
<div class="h5"> On 11/02/2012 12:41 AM, francesca
vitalini wrote:
<blockquote type="cite">In order to overcome the problem
I tried to fix everything except the backbone
(solvent, sidechain and CA, as I want the structure to
be maintained). However, if I do then I have problems
with the energy minimization as the force on the 15300
is infinite.<br>
<br>
Getting Loaded...<br>
Reading file EM1-1.tpr, VERSION 3.3.1 (single
precision)<br>
Loaded with Money<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+01<br>
Number of steps = 2000<br>
-------------------------------------------------------
inf, atom= 15300<br>
Program mdrun, VERSION 3.3.1<br>
Source code file: nsgrid.c, line: 226<br>
<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each
particle to a grid<br>
based on its coordinates. If your system contains
collisions or parameter<br>
errors that give particles very high velocities you
might end up with some<br>
coordinates being +-Infinity or NaN (not-a-number).
Obviously, we cannot<br>
put these on a grid, so this is usually where we
detect those errors.<br>
Make sure your system is properly energy-minimized and
that the potential<br>
energy seems reasonable before trying again.<br>
<br>
Variable ci has value -<a moz-do-not-send="true"
href="tel:2147483648" value="+12147483648"
target="_blank">2147483648</a>. It should have been
within [ 0 .. 27744 ]<br>
Please report this to the mailing list (<a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>)<br>
-------------------------------------------------------<br>
<br>
"Oh My God ! It's the Funky Shit" (Beastie Boys)<br>
<br>
Halting program mdrun<br>
<br>
You suggested to check if there is any overlapping.</blockquote>
<br>
</div>
</div>
... so you need to get out some visualization software and
look at the transformed structure :)
<div class="im"><br>
<br>
<blockquote type="cite"> There might be as my structure is
obtained through a reverse transformation from a CG
representation. In the mapping the atoms are positioned
randomly in the bead. Now I'm running some energy
minimization to equilibrate those atoms. I had to
solvate the system after the mapping (couldn't do it
before due to problems with ions)but I haven't
equilibrated it yet and I'm keeping it fixed which could
also be a source of overlapping. <br>
</blockquote>
<br>
</div>
Local minimization with EM cannot in general take a "random"
positioning of the generated atoms and make it one that will
be stable under MD. Some structure knowledge needs to be
build into the reverse transformation.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark</font></span>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"> Any ideas?<br>
Thanks.<br>
Francesca<br>
<br>
<br>
<div class="gmail_quote">2012/2/10 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> I achieve<br>
<br>
Steepest Descents converged to machine
precision in 205 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -1.49131940478719e+07<br>
Maximum force = 1.09664530279637e+06 on
atom 1520 (parto of the protein)<br>
Norm of force = 2.28369808518165e+06<br>
<br>
</blockquote>
<br>
</div>
The magnitude of the force suggests atomic overlap
somewhere. Start by investigating the environment
around atom 1520.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> and the system looked
with vmd doesn't look as if it was exploding.
However, I have warnings about the table
extension and I don't know why but gromacs
writes pdb files sometime. However I thought
that there <br>
</blockquote>
<br>
</div>
The "step.pdb" files are written when mdrun is
about to crash.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> might have been an
error in the way I defined the position
restraints, in fact in the mdp file I hade
define = -DEPOSRE while in the topology I had
ifdef DEFINE_WAT, so it might have moved it
all without fixing the water. So I tried again
and this time I got<br>
<br>
</blockquote>
<br>
</div>
The "define" statements are literal, so be careful
of typos. -DEPOSRE will not work when the
topology calls for -DPOSRES. So unless you've
changed default naming for "define" statements,
you're not going to get what you expect.
<div> <br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> Steepest Descents
converged to machine precision in 72 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -2.0135496e+07<br>
Maximum force = 2.0486184e+12 on atom
4479<br>
Norm of force = 7.2424045e+13<br>
<br>
</blockquote>
<br>
</div>
Again, symptomatic of severe atomic overlap.
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> but again the same
issue with table extent and still the
production of pdb files.<br>
<br>
Any explanations?<br>
<br>
</blockquote>
<br>
</div>
Investigate the starting configurations near the
problematic atoms.<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System</a><span><font
color="#888888"><br>
<br>
-Justin</font></span>
<div>
<div><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a>
| <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080"
value="+15402319080" target="_blank">(540)
231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br clear="all">
<br>
-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group,
<br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
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-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group, <br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
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