<div>Hi,</div><div><br></div><div><b><u>Here's to tidy up my earlier query which has gotten a bit messy</u> -- to include the earlier previous relevant informations that were asked, and to provide additional relevant informations.</b></div>
<div><br></div><div><div>I've tried running NEMD test-runs in NPT vis initially setting the "<span lang="EN-AU">cos_acceleration = 0.3" (</span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">nm ps^-2)</span> parameter to determine the solvent viscosity.</div>
<div><span lang="EN-AU">However my system kept spectacularly exploding. </span>My system is stable under normal MD (up to 30% over its empirical boiling point at 490K).</div><div><span style="font-size: x-small; "><br></span></div>
<div><span style="font-size: x-small; "><span class="Apple-style-span" style="font-size: small; ">My system is stable when cos_acceleration is below ~0.05, etc. <b>However I still keep getting <u>ZERO</u> for </b></span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; "><b>both 2CosZ*Vel-X and 1/Viscosity</b> out of all the</span><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; "> test runs (including those that exploded) as showing below in the g_energy output and also in the .xvg file.</span></div>
<div><span class="Apple-style-span" style="font-size: x-small;"><br></span></div></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>Statistics over 3515501 steps [ 2000.0000 through 9031.0000 ps ], 20 data sets</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>All statistics are over 351551 points</div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><br></div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>Energy Average Err.Est. RMSD Tot-Drift</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>-------------------------------------------------------------------------------</div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>Angle 2105.24 1.9 74.6742 11.9145 (kJ/mol)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>Fourier Dih. -129.198 11 58.6995 -58.4497 (kJ/mol)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>...</div></blockquote>
<blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>Total Energy -64836.9 7.5 192.87 -45.1406 (kJ/mol)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>Temperature 297.941 0.012 6.87995 -0.042248 (K)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>Pressure 1.02384 0.025 381.044 -0.0603063 (bar)</div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>Volume 42.8729 0.0059 0.468899 -0.00248636 (nm^3)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div>Density 940.264 0.13 10.2704 0.0530898 (kg/m^3)</div></blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>Enthalpy -64836.6 7.5 192.87 -45.1406 (kJ/mol)</div>
</blockquote><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>2CosZ*Vel-X 0 0 0 0 (nm/ps)</b></div></blockquote>
<blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><b>1/Viscosity 0 0 0 0 (m s/kg)</b></div></blockquote></blockquote>
<div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">---------------------------------</span></div><div><div><div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">
<br></div></div></div><div><div><div></div><div><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><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: x-small; border-collapse: collapse; "><br>
</span></div><div><font face="arial, sans-serif"><span style="border-collapse: collapse; "><span style="font-size: x-small; "></span></span></font><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: x-small; border-collapse: collapse; "><b>cos_acceleration<span style="white-space: pre-wrap; ">        </span>= 0.05</b></span></div>
</div></div></div></div><div><br></div><div><br></div><div>Are there anything that I need to set to get non-zero output values?</div><div><br></div><div>Cheers,</div><div>Junqiao LEE (Wade)</div>