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On 19/01/2011 7:33 AM, TJ Mustard wrote:
<blockquote
cite="mid:248910379.7786.1295382796540.JavaMail.open-xchange@oxusgw00.lxa.perfora.net"
type="cite">
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<title></title>
<p style="margin: 0px;"><span> </span></p>
<div style="margin: 5px 0px;"> <br>
On January 17, 2011 at 3:48 PM Mark Abraham
<a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a> wrote:<br>
<br>
<blockquote type="cite" style="margin-left: 0px; padding-left:
10px; border-left: 1px solid blue;"> On 18/01/2011 10:27 AM,
TJ Mustard wrote:
<blockquote type="cite">
<p style="margin: 0px;"><span> </span></p>
<div style="margin: 5px 0px;"> <br>
On January 17, 2011 at 2:47 PM TJ Mustard <a
moz-do-not-send="true"
href="mailto:mustardt@onid.orst.edu"><mustardt@onid.orst.edu></a>
wrote:<br>
<br>
<blockquote type="cite" style="margin-left: 0px;
padding-left: 10px; border-left: 1px solid blue;">
<p style="margin: 0px;"><span> </span></p>
<div style="margin: 5px 0px;"> On January 17, 2011 at
2:21 PM "Justin A. Lemkul" <a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
wrote:<br>
<br>
><br>
><br>
> TJ Mustard wrote:<br>
> ><br>
> ><br>
> > No this is a completely different error that
occurs when the other (EM)<br>
> > error does not.<br>
> ><br>
><br>
> So, EM completes, but you then get this unstable
system? How well did EM<br>
> converge? Were the potential and maximum force
acceptable?<br>
><br>
> Instabilities are generally caused by incorrect
topologies or .mdp settings.<br>
> Those are the first places I would look for
sources of error.<br>
><br>
> -Justin<br>
><br>
> > <br>
> ><br>
> > Thank you,<br>
> ><br>
> > TJ Mustard<br>
> ><br>
> > On January 17, 2011 at 1:51 PM "Justin A.
Lemkul" <a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
wrote:<br>
> ><br>
> > ><br>
> > ><br>
> > > TJ Mustard wrote:<br>
> > > ><br>
> > > ><br>
> > > > Hi all,<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > We have been running a lot of
simulations on protein ligand<br>
> > > > interactions, and my
settings/setup/mdp files worked great for one<br>
> > > > system. Then when we moved to a
larger and more complicated system we<br>
> > > > started getting mdrun 1-4
interaction errors in our MD.<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > We are running with heavyh and
have correctly made our ligands with<br>
> > > > acpype and edited to have heavyh.<br>
> > > ><br>
> > > > Same setup as our smaller simpler
model, but keep getting these:<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > Warning: 1-4 interaction between
X and Y at distance 1.804 which is<br>
> > > > larger than 1-4 table size 1.800
nm.<br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > > The jobs will continue on and
finish but we are worried about the error<br>
> > > > that could be included with these
errors.<br>
> > > ><br>
> > > ><br>
> > ><br>
> > > Is this related to the other issue
we're discussing? If so, please<br>
> > do not<br>
> > > double-post, especially if you're
including different information in<br>
> > different<br>
> > > threads. It becomes a nightmare to
try to keep track of.<br>
> > ><br>
> > > That particular error is usually not a
good sign. Normal, stable<br>
> > simulations<br>
> > > should not give such an error.<br>
> > ><br>
> > > -Justin<br>
> > > </div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Here is the tail of my em:</p>
<p style="margin: 0px;">Step= 3438, Dmax= 2.5e-04 nm,
Epot= -1.05878e+06 Fmax= 8.91784e+01, atom= 43563<br>
Step= 3439, Dmax= 3.0e-04 nm, Epot= -1.05878e+06 Fmax=
8.89898e+01, atom= 43563<br>
Step= 3440, Dmax= 3.6e-04 nm, Epot= -1.05878e+06 Fmax=
3.27390e+02, atom= 24<br>
Step= 3441, Dmax= 4.3e-04 nm, Epot= -1.05878e+06 Fmax=
3.34235e+02, atom= 24<br>
Step= 3451, Dmax= 1.0e-06 nm, Epot= -1.05878e+06 Fmax=
3.32604e+02, atom= 24563<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 20<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy,
or turn<br>
off constraints alltogether (set constraints = none in
mdp file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in
3452 steps,<br>
but did not reach the requested Fmax < 20.<br>
Potential Energy = -1.0587850e+06<br>
Maximum force = 3.3423511e+02 on atom 24<br>
Norm of force = 4.9464898e+00</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">My major settings are:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">define =
-DPOSRES_WATER</p>
<p style="margin: 0px;">integrator = steep</p>
<p style="margin: 0px;">nsteps = 10000</p>
<p style="margin: 0px;">emtol = 20 <br>
emstep = 0.01</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Am I setting my emtol to low? I
occasionally see a Fmax of ~250-900 but mostly above
that.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I am currently having the
epiphany that -DPOSRES_WATER could be my problem.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Thank you,</p>
<p style="margin: 0px;">TJ Mustard</p>
<p style="margin: 0px;"> </p>
</blockquote>
</div>
<p style="margin: 0px;">OK I ran the EM without the
-DPOSRES_WATER defined and continued through my script to
pr and md, and I got this error on my first MD after a
positional restraint md (we call it a PR).</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">First the EM tail:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Step= 5519, Dmax= 8.3e-04 nm, Epot=
-1.09261e+06 Fmax= 8.13679e+02, atom= 24<br>
Step= 5520, Dmax= 1.0e-03 nm, Epot= -1.09261e+06 Fmax=
7.21335e+02, atom= 24<br>
Step= 5523, Dmax= 3.0e-04 nm, Epot= -1.09261e+06 Fmax=
2.58642e+02, atom= 24<br>
Step= 5527, Dmax= 4.5e-05 nm, Epot= -1.09261e+06 Fmax=
1.88718e+02, atom= 24936<br>
Step= 5533, Dmax= 1.7e-06 nm, Epot= -1.09261e+06 Fmax=
1.86052e+02, atom= 24<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 20<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or
turn<br>
off constraints alltogether (set constraints = none in mdp
file)<br>
<br>
writing lowest energy coordinates.<br>
<br>
Steepest Descents converged to machine precision in 5534
steps,<br>
but did not reach the requested Fmax < 20.<br>
Potential Energy = -1.0926141e+06<br>
Maximum force = 1.8871829e+02 on atom 24<br>
Norm of force = 4.8353853e+00</p>
</blockquote>
<br>
That looks fine.<br>
<br>
<blockquote type="cite">
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Now the MD tail:</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">No previous checkpoint file present,
assuming this is a new run.<br>
<br>
Back Off! I just backed up md.log to ./#md.log.1#<br>
Getting Loaded...<br>
Reading file RFP-t_md.tpr, VERSION 4.5.3 (single
precision)<br>
Starting 2 threads<br>
Loaded with Money<br>
<br>
Making 1D domain decomposition 2 x 1 x 1<br>
starting mdrun 'ligand in water'<br>
25000 steps, 100.0 ps.<br>
step 10400, will finish Mon Jan 17 15:51:43 2011Warning:
1-4 interaction between 108 and 116 at distance 1.800
which is larger than the 1-4 table size 1.800 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp
file<br>
or with user tables increase the table size<br>
step 11700, will finish Mon Jan 17 15:52:10 2011imb F 0%</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Any thoughts? Remember this system
is doing FEP and heavy hydrogens.</p>
</blockquote>
<br>
Simplify things while troubleshooting. Does normal MD work
instead of FEP? Do normal hydrogens work?<br>
<br>
Use nstxout = 1 and look and the region around atoms 108 116
to see what is breaking. That may tell you why it is breaking.<br>
<br>
<blockquote type="cite">
<p style="margin: 0px;">But so was the positional restraint
md, and it did not error.</p>
</blockquote>
<br>
Shrug, numerical instabilities can take time to show up.<br>
<br>
Mark<br>
</blockquote>
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I have ran both light hydrogen with and
without FEP on and yes the runs with the FEP give the 1-4
interaction errors. I will soon be running Heavy w/o FEP. The
other very interesting part is that 108 and 116 are 17.2
Angstroms apart. They are on the same molecule(drug) but very
far apart and definitely not bonded.</p>
</blockquote>
<br>
Something's impossible there. 1-4 interactions can arise only when
three bonds connect the atoms. What's your drug topology?<br>
<br>
<blockquote
cite="mid:248910379.7786.1295382796540.JavaMail.open-xchange@oxusgw00.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">Also my rvdw, rlist, and rcoulomb are all
0.8, which is to my knowledge 8 angstroms. How are two
particles, though on the same molecule, interacting outside the
PME/Cut-off distance?</p>
</blockquote>
<br>
1-4 interactions have nothing to do with PME or cut-offs. See manual
4.6.1.<br>
<br>
Also, such short cut-offs need compensating changes in ewald_rtol
and fourier_spacing. 1.0nm with 1e-5 and 0.12nm are normal,
well-tested values.<br>
<blockquote
cite="mid:248910379.7786.1295382796540.JavaMail.open-xchange@oxusgw00.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">And if this is a problem do I need to
increase my PME/Cut-off distance such that the entire molecule
is within that distance. I would rather not, due to speed
issues.</p>
</blockquote>
<br>
Certainly not, even if it was relevant :-)<br>
<br>
Mark<br>
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