<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 20/01/2011 9:53 AM, TJ Mustard wrote:
<blockquote
cite="mid:1214304766.5867.1295477591236.JavaMail.open-xchange@oxusgw02.lxa.perfora.net"
type="cite">
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
<title></title>
<p style="margin: 0px;"><span> </span></p>
<div style="margin: 5px 0px;"> <br>
On January 18, 2011 at 12:50 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 19/01/2011 7:33 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 3:48 PM Mark Abraham <a
moz-do-not-send="true"
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 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 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>
</blockquote>
</div>
<p style="margin: 0px;">Mark and all,</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">This</p>
</blockquote>
<br>
To what does "this" refer?<br>
<br>
<blockquote
cite="mid:1214304766.5867.1295477591236.JavaMail.open-xchange@oxusgw02.lxa.perfora.net"
type="cite">
<p style="margin: 0px;"> has fixed the 1-4 interaction errors but
has cause dynamic load balancing to be turned on. What can be
done to, other than smaller pme/cut-offs to limit dynamic load
balancing? While still keeping the precision of course.</p>
</blockquote>
<br>
See mdrun -h for the dynamic load-balancing control. But why do you
want to turn it off? Performance is better with it on.<br>
<br>
Mark<br>
</body>
</html>