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On 2/02/2012 3:36 PM, Alex Seling wrote:
<blockquote
cite="mid:CAHq4TGTxc_iC4vjtFfu9DpRzJKET3bZhwAQAm40GnUvBRa-CSg@mail.gmail.com"
type="cite">Hello,
<div><br>
</div>
<div>I've recently been having trouble with my simulations blowing
up. Specifically,</div>
<div><br>
</div>
<div style="">"This usually means your system is exploding,</div>
<div style="">if not, you should increase table-extension in your
mdp file</div>
<div style="">or with user tables increase the table size" <br>
</div>
<div style=""><br>
</div>
<div><span style="">for a few interactions, with each of them
approaching inf.</span></div>
</blockquote>
<br>
The usual advice and diagnostic procedure can be found here
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
<blockquote
cite="mid:CAHq4TGTxc_iC4vjtFfu9DpRzJKET3bZhwAQAm40GnUvBRa-CSg@mail.gmail.com"
type="cite">
<div><span style=""><br>
</span></div>
<div>Can anyone find anything glaringly wrong with my .mdp?</div>
</blockquote>
<br>
No constraints often requires a time step of 0.0005ps.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHq4TGTxc_iC4vjtFfu9DpRzJKET3bZhwAQAm40GnUvBRa-CSg@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>Thanks,</div>
<div>Alex Seling</div>
<div><br>
</div>
<div>
<div>title = Minimization of alpha-synuclein</div>
<div>cpp = /lib/cpp -traditional</div>
<div>define = -DFLEXIBLE</div>
<div>integrator = sd</div>
<div>
constraints = none </div>
<div>tinit = 0</div>
<div>dt = 0.001</div>
<div>nsteps = 1000000</div>
<div>emtol = 0.00001 </div>
<div>emstep = 0.1 </div>
<div>nstcgsteep = 1000</div>
<div>bd-fric = 0</div>
<div>nstlog = 50</div>
<div>
nstenergy = 1 </div>
<div>gen_temp = 273</div>
<div>gb_epsilon_solvent = 78.3</div>
<div>implicit_solvent = GBSA</div>
<div>gb_algorithm = Still</div>
<div>nstcomm = 10</div>
<div>xtc_precision = 1000</div>
<div>gen_vel = yes</div>
<div>nstxtcout = 0</div>
<div>nstxout = 100</div>
<div>pbc = no</div>
<div>energygrps = system</div>
<div>nstfout = 0</div>
<div>nstvout = 0</div>
<div>niter = 20</div>
<div>nstlist = 10</div>
</div>
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</blockquote>
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