<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><span class="Apple-style-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 class="Apple-style-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 class="Apple-style-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 class="Apple-style-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 class="Apple-style-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><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; "><span class="Apple-style-span" style="font-size: x-small;">integrator = md</span></span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">dt = 0.002 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nsteps = 100000</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">comm-mode = Linear</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstcomm = 10</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstxout = 10000</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstvout = 10000</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstfout = 0 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstlog = 500</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstcalcenergy<span class="Apple-tab-span" style="white-space:pre"> </span> = 250 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstenergy = 500</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstxtcout = 500</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">nstlist = 10</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">ns_type = grid </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">pbc = xyz</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">coulombtype = pme</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">rlist = 1.0</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">rcoulomb = 1.0 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">vdw-type = Cut-off</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">rvdw = 1.0</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">pcoupl = Parrinello-Rahman</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">pcoupltype = isotropic</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">tau_p = 1.0</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">compressibility = 4.5e-5</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">ref_p = 0.5</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">Tcoupl = v-rescale</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">tc_grps = System </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">tau_t = 0.1 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">ref_t = 298</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">gen_vel = no </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">gen_seed = 94839 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">constraints = All-bonds</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">constraint-algorithm = lincs</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;"><br></span></span></font></div><div>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">; acc_grps<span class="Apple-tab-span" style="white-space:pre"> </span>= MMA1 MMA53 MMA97 MMA123 MMA167 MMA197 MMA227 </span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">accelerate<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.1</span></span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><span class="Apple-style-span" style="font-size: x-small;">cos_acceleration<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.01</span></span></font></div>
</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; "><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 style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br></div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">On 14/11/2010 2:42 AM, Junqiao Lee wrote:</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> Running the simulation in NVT doesn't seem to work too.</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> And (other than the system not blowing up now) similar to the NPT</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> test runs were 0.</span></font><br>
<br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Is the starting configuration stable under normal MD?</span></font><br><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Mark</span></font><span class="Apple-style-span" style="font-size: x-small; "><br>
</span><span class="Apple-style-span" style="font-size: x-small; "><br></span><div class="gmail_quote"><span class="Apple-style-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">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 class="Apple-style-span" style="font-size: x-small;">Running the simulation in NVT doesn't seem to work too.</span></div>
<div><span class="Apple-style-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 class="h5">
<div><span class="Apple-style-span" style="font-size: x-small;"><br></span></div>
<div><span class="Apple-style-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 class="Apple-style-span" style="font-size: x-small;">Hi,</span></div>
<div><span class="Apple-style-span" style="font-size: x-small;"><br></span></div>
<div><span class="Apple-style-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 class="Apple-style-span" style="font-size: x-small;">However my system kept spectacularly exploding.</span></span><span class="Apple-style-span" style="font-size: x-small; "> </span></div>
<div><span lang="EN-AU"><span class="Apple-style-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 class="Apple-style-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 class="Apple-style-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 class="Apple-style-span" style="font-size: x-small;">Thanks for the help.</span></span></div>
<div><span lang="EN-AU"><span class="Apple-style-span" style="font-size: x-small;">Cheers,</span></span></div>
<div><span lang="EN-AU"><span class="Apple-style-span" style="font-size: x-small;">Junqiao LEE (Wade)</span></span></div><font color="#888888"><span class="Apple-style-span" style="font-size: x-small;">
</span><div><span lang="EN-AU"><span class="Apple-style-span" style="font-size: x-small;">Curtin University<br>Dept. of Chem. [NRI]</span></span></div></font></blockquote></div></div></div></blockquote></div>