I'm currently using Gromacs 4.5.1<div>My system is stable up to 490K before it blows up under normal MD.</div><div>Cheers, Jun (Wade)</div><div><br><div class="gmail_quote">On Sun, Nov 14, 2010 at 12:14 AM, Junqiao Lee <span dir="ltr"><<a href="mailto:aeondrift@gmail.com">aeondrift@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Woops, btw please ignore the lines:<div><div class="im"><span style="font-family:arial, sans-serif;font-size:x-small;border-collapse:collapse">; acc_grps<span style="white-space:pre-wrap"> </span>= MMA1 MMA53 MMA97 MMA123 MMA167 MMA197 MMA227 </span><div>
<font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">accelerate<span style="white-space:pre-wrap"> </span>= 0.1</span></span></font></div></div><div><span style="font-family:arial, sans-serif;border-collapse:collapse">in the parameters pasted earlier.</span></div>
<div><span style="font-family:arial, sans-serif;border-collapse:collapse"><br></span></div><div><span style="font-family:arial, sans-serif;border-collapse:collapse">They were not present in my initial test-runs. I was just trying out alternatives...</span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small"><br></span></span></font></div><br><div class="gmail_quote"><div><div></div><div class="h5">On Sun, Nov 14, 2010 at 12:13 AM, Junqiao Lee <span dir="ltr"><<a href="mailto:aeondrift@gmail.com" target="_blank">aeondrift@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5"><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
<span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">Hi Mark,</span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br></span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">Yes my starting configuration is stable under normal MD.</span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br></span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">I've since reduced cos_acceleration to 0.01 (</span>nm ps^-2).</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">It seems to be holding together, however both <b>2CosZ*Vel-X</b> and <b>1/Viscosity</b> that I've got out of the test runs (with the <i>g_energy</i> program) remained at the value of 0 (as before). Perhaps I'll still need to specify something else that I might have missed, which I can't seem to find in the manual (still flipping through)?</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">I've included my run-input parameters below in-case that'll be helpful. =)</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Thanks heaps for the help!</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">---------------------------------</div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div></div></div><div><div><div></div><div class="h5"><div><span style="font-family:arial, sans-serif;border-collapse:collapse"><span style="font-size:x-small">integrator = md</span></span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">dt = 0.002 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nsteps = 100000</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">comm-mode = Linear</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstcomm = 10</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstxout = 10000</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstvout = 10000</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstfout = 0 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstlog = 500</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstcalcenergy<span style="white-space:pre-wrap"> </span> = 250 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstenergy = 500</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstxtcout = 500</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">nstlist = 10</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">ns_type = grid </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">pbc = xyz</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">coulombtype = pme</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">rlist = 1.0</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">rcoulomb = 1.0 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">vdw-type = Cut-off</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">rvdw = 1.0</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">pcoupl = Parrinello-Rahman</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">pcoupltype = isotropic</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">tau_p = 1.0</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">compressibility = 4.5e-5</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">ref_p = 0.5</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">Tcoupl = v-rescale</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">tc_grps = System </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">tau_t = 0.1 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">ref_t = 298</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">gen_vel = no </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">gen_seed = 94839 </span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">constraints = All-bonds</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">constraint-algorithm = lincs</span></span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small"><br></span></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse;font-size:x-small"><br>
</span></font></div>
</div></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><span style="font-size:x-small">cos_acceleration<span style="white-space:pre-wrap"> </span>= 0.01</span></span></font></div>
</div><div><div></div><div class="h5"><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
Cheers </div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Jun (Wade)</div><div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div>
<font face="arial, sans-serif"><span style="border-collapse:collapse">On 14/11/2010 2:42 AM, Junqiao Lee wrote:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Running the simulation in NVT doesn't seem to work too.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> And (other than the system not blowing up now) similar to the NPT</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> test runs were 0.</span></font><br>
<br></div><font face="arial, sans-serif"><span style="border-collapse:collapse">Is the starting configuration stable under normal MD?</span></font><br><br><font face="arial, sans-serif"><span style="border-collapse:collapse">Mark</span></font><div>
<div></div><div><span style="font-size:x-small"><br>
</span><span style="font-size:x-small"><br></span><div class="gmail_quote"><span style="font-size:x-small">On Sat, Nov 13, 2010 at 11:42 PM, Junqiao Lee <span dir="ltr"><<a href="mailto:aeondrift@gmail.com" target="_blank">aeondrift@gmail.com</a>></span> wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><span style="font-size:x-small">Running the simulation in NVT doesn't seem to work too.</span></div>
<div><span style="font-size:x-small">And (other than the system not blowing up now) similar to the NPT simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the test runs were 0.</span></div>
<div><div></div><div>
<div><span style="font-size:x-small"><br></span></div>
<div><span style="font-size:x-small">On Sat, Nov 13, 2010 at 11:17 PM, Junqiao Lee <span dir="ltr"><<a href="mailto:aeondrift@gmail.com" target="_blank">aeondrift@gmail.com</a>></span> wrote:<br>
</span></div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="padding-left:1ex;margin:0px 0px 0px 0.8ex;border-left:#ccc 1px solid">
<div><span style="font-size:x-small">Hi,</span></div>
<div><span style="font-size:x-small"><br></span></div>
<div><span style="font-size:x-small">I've tried running an NEMD run in NPT vis setting the "<span lang="EN-AU">cos_acceleration = 0.3" parameter to determine the solvent viscosity.</span></span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">However my system kept spectacularly exploding.</span></span><span style="font-size:x-small"> </span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">I've also tried running with the acc_grps specified for 7 molecules (out of the 250 within the system), but it still didn't work.</span></span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">cos_acceleration = ~0.3 nm ps^-2 seem like a reasonable value to use?</span></span></div><div><span lang="EN-AU"><span style="font-size:x-small">Am I only restricted to running NEMD calcs. in NVT?</span></span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">Thanks for the help.</span></span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">Cheers,</span></span></div>
<div><span lang="EN-AU"><span style="font-size:x-small">Junqiao LEE (Wade)</span></span></div><font color="#888888"><span style="font-size:x-small">
</span><div><span lang="EN-AU"><span style="font-size:x-small">Curtin University<br>Dept. of Chem. [NRI]</span></span></div></font></blockquote></div></div></div></blockquote></div>
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