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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Why can’t you energy minimise the water block / film in the final box size?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>And you can’t simply change the cut-offs like that to suit your box size, you need to use the settings that the forcefield was parameterised for, or what others have studied / published and found to be suitable. You can’t swap and changes those settings at a whim.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Catch ya,<br><br>Dr. Dallas Warren<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>, Monash University<br>381 Royal Parade, Parkville VIC 3010<br>dallas.warren@monash.edu<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>+61 3 9903 9304<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>gromacs<br><b>Sent:</b> Friday, 17 December 2010 11:32 AM<br><b>To:</b> gmx-users@gromacs.org<br><b>Subject:</b> [gmx-users] water genbox 3x3x0.8 EM not successful T too high<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><pre><br>>Message:<span style='font-family:"Courier New"'> </span>3<o:p></o:p></pre><pre>>Date:<span style='font-family:"Courier New"'> </span>Thu,<span style='font-family:"Courier New"'> </span>16<span style='font-family:"Courier New"'> </span>Dec<span style='font-family:"Courier New"'> </span>2010<span style='font-family:"Courier New"'> </span>11:50:51<span style='font-family:"Courier New"'> </span>-0500<o:p></o:p></pre><pre>>From:<span style='font-family:"Courier New"'> </span>Vitaly<span style='font-family:"Courier New"'> </span>Chaban<span style='font-family:"Courier New"'> </span><vvchaban@gmail.com><o:p></o:p></pre><pre>>Subject:<span style='font-family:"Courier New"'> </span>[gmx-users]<span style='font-family:"Courier New"'> </span>Re:<span style='font-family:"Courier New"'> </span>water<span style='font-family:"Courier New"'> </span>genbox<span style='font-family:"Courier New"'> </span>3x3x0.8<span style='font-family:"Courier New"'> </span>EM<span style='font-family:"Courier New"'> </span>not<span style='font-family:"Courier New"'> </span>successful<span style='font-family:"Courier New"'> </span>T<span style='font-family:"Courier New"'> </span>not<o:p></o:p></pre><pre>> high<o:p></o:p></pre><pre>>To:<span style='font-family:"Courier New"'> </span>gmx-users@gromacs.org<o:p></o:p></pre><pre>>Cc:<span style='font-family:"Courier New"'> </span>gromacs<span style='font-family:"Courier New"'> </span><ptf1242@163.com><o:p></o:p></pre><pre>>Message-ID:<o:p></o:p></pre><pre>> <AANLkTikYKV=-oEV10BxgYs5N_nMqxbonwbHxkybuHJQd@mail.gmail.com><o:p></o:p></pre><pre>>Content-Type:<span style='font-family:"Courier New"'> </span>text/plain;<span style='font-family:"Courier New"'> </span>charset=ISO-8859-1<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>From:<span style='font-family:"Courier New"'> </span>gromacs<span style='font-family:"Courier New"'> </span><ptf1242@163.com><o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Subject:<span style='font-family:"Courier New"'> </span>[gmx-users]<span style='font-family:"Courier New"'> </span>water<span style='font-family:"Courier New"'> </span>genbox<span style='font-family:"Courier New"'> </span>3x3x0.8<span style='font-family:"Courier New"'> </span>EM<span style='font-family:"Courier New"'> </span>not<span style='font-family:"Courier New"'> </span>successful<span style='font-family:"Courier New"'> </span>T<span style='font-family:"Courier New"'> </span>not<span style='font-family:"Courier New"'> </span>high<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Hi,<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>I<span style='font-family:"Courier New"'> </span>want<span style='font-family:"Courier New"'> </span>to<span style='font-family:"Courier New"'> </span>simulate<span style='font-family:"Courier New"'> </span>3x3x0.8<span style='font-family:"Courier New"'> </span>water<span style='font-family:"Courier New"'> </span>film<span style='font-family:"Courier New"'> </span>(bulk<span style='font-family:"Courier New"'> </span>water)<span style='font-family:"Courier New"'> </span>first<span style='font-family:"Courier New"'> </span>creat<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>water,<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>genbox<span style='font-family:"Courier New"'> </span>-cs<span style='font-family:"Courier New"'> </span>-o<span style='font-family:"Courier New"'> </span>film.gro<span style='font-family:"Courier New"'> </span>-box<span style='font-family:"Courier New"'> </span>3<span style='font-family:"Courier New"'> </span>3<span style='font-family:"Courier New"'> </span>0.8<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>then,<span style='font-family:"Courier New"'> </span>i<span style='font-family:"Courier New"'> </span>EM<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>bulk<span style='font-family:"Courier New"'> </span>water;<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Using<span style='font-family:"Courier New"'> </span>steep,<span style='font-family:"Courier New"'> </span>but<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>t<span style='font-family:"Courier New"'> </span>=<span style='font-family:"Courier New"'> </span>0.011<span style='font-family:"Courier New"'> </span>ps:<span style='font-family:"Courier New"'> </span>Water<span style='font-family:"Courier New"'> </span>molecule<span style='font-family:"Courier New"'> </span>starting<span style='font-family:"Courier New"'> </span>at<span style='font-family:"Courier New"'> </span>atom<span style='font-family:"Courier New"'> </span>298<span style='font-family:"Courier New"'> </span>can<span style='font-family:"Courier New"'> </span>not<span style='font-family:"Courier New"'> </span>be<span style='font-family:"Courier New"'> </span>settled.<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Check<span style='font-family:"Courier New"'> </span>for<span style='font-family:"Courier New"'> </span>bad<span style='font-family:"Courier New"'> </span>contacts<span style='font-family:"Courier New"'> </span>and/or<span style='font-family:"Courier New"'> </span>reduce<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>timestep.<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Wrote<span style='font-family:"Courier New"'> </span>pdb<span style='font-family:"Courier New"'> </span>files<span style='font-family:"Courier New"'> </span>with<span style='font-family:"Courier New"'> </span>previous<span style='font-family:"Courier New"'> </span>and<span style='font-family:"Courier New"'> </span>current<span style='font-family:"Courier New"'> </span>coordinates<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>then<span style='font-family:"Courier New"'> </span>i<span style='font-family:"Courier New"'> </span>run,<span style='font-family:"Courier New"'> </span>and<span style='font-family:"Courier New"'> </span>i<span style='font-family:"Courier New"'> </span>get<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>result.<span style='font-family:"Courier New"'> </span>I<span style='font-family:"Courier New"'> </span>use<span style='font-family:"Courier New"'> </span>NPT,<span style='font-family:"Courier New"'> </span>and<span style='font-family:"Courier New"'> </span>T=300K.<span style='font-family:"Courier New"'> </span>I<span style='font-family:"Courier New"'> </span>run<span style='font-family:"Courier New"'> </span>several<span style='font-family:"Courier New"'> </span>times,<span style='font-family:"Courier New"'> </span>but<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>final<span style='font-family:"Courier New"'> </span>T<span style='font-family:"Courier New"'> </span>was<span style='font-family:"Courier New"'> </span>still<span style='font-family:"Courier New"'> </span>411K.<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><o:p> </o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>So<span style='font-family:"Courier New"'> </span>what<span style='font-family:"Courier New"'> </span>could<span style='font-family:"Courier New"'> </span>i<span style='font-family:"Courier New"'> </span>do<span style='font-family:"Courier New"'> </span>to<span style='font-family:"Courier New"'> </span>get<span style='font-family:"Courier New"'> </span>EM<span style='font-family:"Courier New"'> </span>process<span style='font-family:"Courier New"'> </span>successful?<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>And<span style='font-family:"Courier New"'> </span>what<span style='font-family:"Courier New"'> </span>is<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>reason<span style='font-family:"Courier New"'> </span>?<span style='font-family:"Courier New"'> </span>why<span style='font-family:"Courier New"'> </span>i<span style='font-family:"Courier New"'> </span>can<span style='font-family:"Courier New"'> </span>not<span style='font-family:"Courier New"'> </span>control<span style='font-family:"Courier New"'> </span>the<span style='font-family:"Courier New"'> </span>T<span style='font-family:"Courier New"'> </span>300K?<o:p></o:p></pre><pre>>><o:p> </o:p></pre><pre>>><o:p> </o:p></pre><pre>>><o:p> </o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Energy<span style='font-family:"Courier New"'> </span>Average<span style='font-family:"Courier New"'> </span>RMSD<span style='font-family:"Courier New"'> </span>Fluct.<span style='font-family:"Courier New"'> </span>Drift<span style='font-family:"Courier New"'> </span>Tot-Drift<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>-------------------------------------------------------------------------------<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Potential<span style='font-family:"Courier New"'> </span>-9496.38<span style='font-family:"Courier New"'> </span>136.145<span style='font-family:"Courier New"'> </span>135.455<span style='font-family:"Courier New"'> </span>-0.158085<span style='font-family:"Courier New"'> </span>-47.4256<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Kinetic<span style='font-family:"Courier New"'> </span>En.<span style='font-family:"Courier New"'> </span>2358.2<span style='font-family:"Courier New"'> </span>73.5876<span style='font-family:"Courier New"'> </span>73.5471<span style='font-family:"Courier New"'> </span>-0.0281891<span style='font-family:"Courier New"'> </span>-8.45676<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Total<span style='font-family:"Courier New"'> </span>Energy<span style='font-family:"Courier New"'> </span>-7138.19<span style='font-family:"Courier New"'> </span>136.284<span style='font-family:"Courier New"'> </span>135.326<span style='font-family:"Courier New"'> </span>-0.186274<span style='font-family:"Courier New"'> </span>-55.8824<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Temperature<span style='font-family:"Courier New"'> </span>411.945<span style='font-family:"Courier New"'> </span>12.8548<span style='font-family:"Courier New"'> </span>12.8477<span style='font-family:"Courier New"'> </span>-0.00492426<span style='font-family:"Courier New"'> </span>-1.47728<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Pressure<span style='font-family:"Courier New"'> </span>(bar)<span style='font-family:"Courier New"'> </span>-1.66406<span style='font-family:"Courier New"'> </span>704.355<span style='font-family:"Courier New"'> </span>704.355<span style='font-family:"Courier New"'> </span>-0.00424907<span style='font-family:"Courier New"'> </span>-1.27473<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Box-X<span style='font-family:"Courier New"'> </span>2.91791<span style='font-family:"Courier New"'> </span>0.0128965<span style='font-family:"Courier New"'> </span>0.0128789<span style='font-family:"Courier New"'> </span>-7.7826e-06<span style='font-family:"Courier New"'> </span>-0.00233479<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Box-Y<span style='font-family:"Courier New"'> </span>2.91791<span style='font-family:"Courier New"'> </span>0.0128965<span style='font-family:"Courier New"'> </span>0.0128789<span style='font-family:"Courier New"'> </span>-7.7826e-06<span style='font-family:"Courier New"'> </span>-0.00233479<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Box-Z<span style='font-family:"Courier New"'> </span>0.778108<span style='font-family:"Courier New"'> </span>0.00343907<span style='font-family:"Courier New"'> </span>0.00343437<span style='font-family:"Courier New"'> </span>-2.07536e-06<span style='font-family:"Courier New"'> </span>-0.000622609<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Density<span style='font-family:"Courier New"'> </span>(SI)<span style='font-family:"Courier New"'> </span>1038.7<span style='font-family:"Courier New"'> </span>13.6165<span style='font-family:"Courier New"'> </span>13.5998<span style='font-family:"Courier New"'> </span>0.00778513<span style='font-family:"Courier New"'> </span>2.33555<o:p></o:p></pre><pre>>><span style='font-family:"Courier New"'> </span>Heat<span style='font-family:"Courier New"'> </span>Capacity<span style='font-family:"Courier New"'> </span>Cv:<span style='font-family:"Courier New"'> </span>12.49<span style='font-family:"Courier New"'> </span>J/mol<span style='font-family:"Courier New"'> </span>K<span style='font-family:"Courier New"'> </span>(factor<span style='font-family:"Courier New"'> </span>=<span style='font-family:"Courier New"'> </span>0.000973754)<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>><o:p> </o:p></pre><pre>><o:p> </o:p></pre><pre>>Hey,<span style='font-family:"Courier New"'> </span>gromacs<span style='font-family:"Courier New"'> </span>-<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>>Nice<span style='font-family:"Courier New"'> </span>to<span style='font-family:"Courier New"'> </span>hear<span style='font-family:"Courier New"'> </span>from<span style='font-family:"Courier New"'> </span>you<span style='font-family:"Courier New"'> </span>here...<span style='font-family:"Courier New"'> </span>It<span style='font-family:"Courier New"'> </span>is<span style='font-family:"Courier New"'> </span>a<span style='font-family:"Courier New"'> </span>bad<span style='font-family:"Courier New"'> </span>idea<span style='font-family:"Courier New"'> </span>to<span style='font-family:"Courier New"'> </span>simulate<span style='font-family:"Courier New"'> </span>something<o:p></o:p></pre><pre>>with<span style='font-family:"Courier New"'> </span>any<span style='font-family:"Courier New"'> </span>cartesian<span style='font-family:"Courier New"'> </span>dimension<span style='font-family:"Courier New"'> </span>lower<span style='font-family:"Courier New"'> </span>than<span style='font-family:"Courier New"'> </span>a<span style='font-family:"Courier New"'> </span>couple<span style='font-family:"Courier New"'> </span>of<span style='font-family:"Courier New"'> </span>nanometers<span style='font-family:"Courier New"'> </span>using<o:p></o:p></pre><pre>>classical<span style='font-family:"Courier New"'> </span>FFs.<span style='font-family:"Courier New"'> </span>All<span style='font-family:"Courier New"'> </span>your<span style='font-family:"Courier New"'> </span>problems<span style='font-family:"Courier New"'> </span>are<span style='font-family:"Courier New"'> </span>generated<span style='font-family:"Courier New"'> </span>by<span style='font-family:"Courier New"'> </span>0.8<span style='font-family:"Courier New"'> </span>nm<span style='font-family:"Courier New"'> </span>of<span style='font-family:"Courier New"'> </span>the<o:p></o:p></pre><pre>>z-side.<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>>--<o:p></o:p></pre><pre>>Dr.<span style='font-family:"Courier New"'> </span>Vitaly<span style='font-family:"Courier New"'> </span>V.<span style='font-family:"Courier New"'> </span>Chaban<o:p></o:p></pre><pre>>Rochester,<span style='font-family:"Courier New"'> </span>U.S.A.<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre>><o:p> </o:p></pre><pre>>------------------------------<o:p></o:p></pre><pre>><o:p> </o:p></pre><pre style='margin-bottom:12.0pt'><br><br>Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK.<br><br>My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface.<br><br>So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success??<br><br><o:p></o:p></pre><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p></div></div></body></html>