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<p style="margin: 0px;"><span> </span></p>
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On January 18, 2011 at 12:50 PM Mark Abraham <Mark.Abraham@anu.edu.au> wrote:<br />
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On 19/01/2011 7:33 AM, TJ Mustard wrote:
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<p style="margin: 0px;"><span> </span></p>
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On January 17, 2011 at 3:48 PM Mark Abraham <a href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a> wrote:<br />
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On 18/01/2011 10:27 AM, TJ Mustard wrote:
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<p style="margin: 0px;"><span> </span></p>
<div style="margin: 5px 0px;">
<br />
On January 17, 2011 at 2:47 PM TJ Mustard <a href="mailto:mustardt@onid.orst.edu"><mustardt@onid.orst.edu></a> wrote:<br />
<br />
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<p style="margin: 0px;"><span> </span></p>
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On January 17, 2011 at 2:21 PM "Justin A. Lemkul" <a 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 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>
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<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>
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<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 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>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Thank you,</p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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