<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><div style="font-size: 14pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: 'times new roman', 'new york', times, serif; "><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt;
font-family: times, serif; "><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div><font class="yiv761359091Apple-style-span" face="times, serif" size="4"><span class="yiv761359091Apple-style-span" style="font-size:16px;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times,
serif" size="6"><span class="yiv761359091Apple-style-span" style="font-size:19px;"><div style="background-color: rgb(255, 255, 255); color: rgb(0, 0, 0); padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; margin-top: 8px; margin-right: 0px; margin-bottom: 0px; margin-left: 12px; display: block; font-size: 14pt; font-family: times, serif; "><div class="yiv761359091yui_3_2_0_34_131722221595052" style="font-size: 14pt; font-family: times, serif; "><div class="yiv761359091yui_3_2_0_34_131722221595057" style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div class="yiv761359091yui_3_2_0_34_131722221595061" style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div class="yiv761359091yui_3_2_0_34_131722221595065" style="font-size: 14pt; font-family: times, serif; "><div class="yiv761359091yui_3_2_0_34_131722221595067" style="font-size: 12pt;
font-family: times, serif; "><div id="yiv761359091"><div class="yiv761359091yui_3_2_0_34_131722221595071" style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">The simulation</span> <span class="yiv761359091hps">box contains just</span></span> water molecules</div><div><br></div><div>** water.pdb **</div><div><div>ATOM 1 OW SOL 1 19.350 2.371 0.000 0.00 0.00 </div><div>ATOM 2 HW1 SOL 1 18.600 2.951 0.000 0.00 0.00 </div><div>ATOM 3 HW2 SOL 1 20.100 2.951
0.000 0.00 0.00 </div><div>END</div><div><div>** md.mdp **</div><div><div>integrator<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= md</div><div>nsteps<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 100000000 <span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>; 200 ns</div><div>dt<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 0.002<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>; 2 fs</div><div>comm-mode = Linear</div><div>ns_type<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= grid</div><div>nstlist<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 5<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>rlist<span
class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 1<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>rcoulomb<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 1<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>rvdw<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 1<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>coulombtype<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= PME<br></div><div>pme_order<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 4<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>fourierspacing<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 0.15</div><div>ewald_rtol = 1e-05</div><div>optimize_fft =
yes</div><div>tcoupl<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= V-rescale<br></div><div>tc-grps<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= System<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>tau_t<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 0.1<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span></div><div>ref_t<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= 300 </div><div>pbc<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= xyz</div><div>vdw-type = Cut-off<br></div><div>gen_vel<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span>= no<span class="yiv761359091Apple-tab-span" style="white-space:pre;"> </span> </div><div>constraints
= all-bonds</div><div>DispCorr = Ener</div><div>constraint-algorithm = Lincs</div><div>lincs-order = 4</div><div>lincs-iter = 1</div><div>lincs-warnangle = 30</div><div>E-z = 1 0.000001 0 ;10 v/cm</div><div><br></div></div></div></div><div><span id="yiv761359091result_box" class="yiv761359091short_text" lang="en"><span class="yiv761359091hps">---- Commands
----</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">pdb2gmx -f water.pdb -posrefc 0</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">Force Field : AMBER99SB-ILDN - Water TIP3P</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">editconf -f conf.gro -bt cubic -box 5 5 5</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span
class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">grompp -f min.mdp -c 5.gro -p topol.top</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">mdrun -s topol.tpr</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span
class="yiv761359091hps">grompp -f
md.mdp -c confout.gro -p topol.top -o md.tpr</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">mdrun -s md.tpr</span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">1. </span></span><span class="yiv761359091Apple-style-span yiv761359091yui_3_2_0_34_1317222215950137" style="font-size: 24px; font-family: arial, sans-serif; "><span class="yiv761359091hps"><span class="yiv761359091Apple-style-span" style="font-size:18px;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif">Whether</font></span></span><span class="yiv761359091Apple-style-span" style="font-size:large;"><font class="yiv761359091Apple-style-span" face="'times new
roman',
'new york', times, serif"> </font></span><span class="yiv761359091hps"><span class="yiv761359091Apple-style-span" style="font-size:large;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif">is</font></span></span><span class="yiv761359091Apple-style-span" style="font-size:large;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif"> </font></span><span class="yiv761359091hps"><span class="yiv761359091Apple-style-span" style="font-size:18px;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif">correct</font></span></span><span class="yiv761359091Apple-style-span" style="font-size:large;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif"> </font></span><span class="yiv761359091hps"><span class="yiv761359091Apple-style-span" style="font-size:large;"><font
class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times,
serif">simulation</font></span></span><span class="yiv761359091Apple-style-span" style="font-size:large;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif"> </font></span><span class="yiv761359091hps"><span class="yiv761359091Apple-style-span" style="font-size:18px;"><font class="yiv761359091Apple-style-span" face="'times new roman', 'new york', times, serif">pure water ?</font></span></span></span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps">2.Chart potential.JPG (</span></span></span></span><span class="hps"><span class="Apple-style-span" style="font-size: 18px; "><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">If</font></span></span><span class="Apple-style-span" style="font-size: large;"><font
class="Apple-style-span" face="'times new roman', 'new york', times, serif"> </font></span><span class="hps"><span class="Apple-style-span" style="font-size: 18px; "><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">request </font></span></span><span class="Apple-style-span" style="font-size: 18px; "><font class="Apple-style-span" face="'times new roman', 'new york', times, serif">، </font></span><span class="yiv761359091hps">attach in next post)</span> <span class="yiv761359091hps">shows</span> <span class="yiv761359091hps">the electric field 0.003 v/nm !?</span> whereas <span class="yiv761359091hps">applied</span> <span class="yiv761359091hps">electric field 0.000001 v/nm in
md.mdp.</span></div><div><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"><span id="yiv761359091result_box" class="yiv761359091" lang="en"><span class="yiv761359091hps"><span id="yiv761359091result_box" class="yiv761359091short_text" lang="en">Do I <span class="yiv761359091hps">wrong in the a</span></span><span class="yiv761359091hps">pplied</span> <span class="yiv761359091hps">electric field 1000 v/m ?</span></span></span></span></span></div></div></div></div></div></div></div></div></div></div></div></span></font></span></font></div><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif; "><div id="yiv761359091"><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-size: 14pt; font-family: times, serif; "><div style="font-size: 14pt; font-family: times, serif; "><div style="font-size: 12pt; font-family: times, serif;
"><br></div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></div><br><br></div></div></div></body></html>