<br /><br /><span>On 28/03/11, <b class="name">Parul tew </b> <parultew@gmail.com> wrote:</span><blockquote cite="mid:AANLkTi=f_neVv44JDcoAV+j6J-CAFTCAmd25RvJ5Q-c8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">Dear GMX users,</span></div>
<div class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;"> I am facing problem while doing energy minimization of the inflated system of a protein with membrane. I inflated the system and updated the removed lipids in the topology file. Now I am stuck during the energy minimization state. Below is the .mdp file for minimization.</span></div>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">; minim_1.mdp - used as input into grompp to generate em_1.tpr</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">integrator<span style=""> </span>= cg<span style=""> </span><span style=""> </span>; Algorithm (cg = conjugate gradient minimization)</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">emtol<span style=""> </span>= 1000.0<span style=""> </span><span style=""> </span>; Stop minimization when the maximum force < 1000.0 kJ/mol/nm</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">emstep<span style=""> </span>= 0.01<span style=""> </span>; Energy step size</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">nsteps<span style=""> </span>= 50000<span style=""> </span>; Maximum number of (minimization) steps to perform</span></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">nstlist<span style=""> </span>= 1<span style=""> </span>; Frequency to update the neighbor list and long range forces</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">ns_type<span style=""> </span>= grid<span style=""> </span>; Method to determine neighbor list (simple, grid)</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">rlist<span style=""> </span>= 1.2<span style=""> </span>; Cut-off for making neighbor list (short range forces)</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">coulombtype= PME<span style=""> </span>; Treatment of long range electrostatic interactions</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">rcoulomb<span style=""> </span>= 1.2<span style=""> </span>; Short-range electrostatic cut-off</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">rvdw<span style=""> </span>= 1.2<span style=""> </span>; Short-range Van der Waals cut-off</span></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><span style="font-family: 'Courier New'; font-size: 10pt;">gen_vel<span style=""> </span><span style=""> </span>= yes</span></p>
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<span style="font-family: 'Courier New'; font-size: 10pt;">define<span style=""> </span>= DSTRONG_POSRES</span></p></div></div></blockquote><br />Your "define" line is wrong. Computers are very exact and you need to be also if you want to succeed at complex computational projects. Go and read in the documentation what the recommended define is.<br /><br /><blockquote cite="mid:AANLkTi=f_neVv44JDcoAV+j6J-CAFTCAmd25RvJ5Q-c8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">when I run this using the command </font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3"><b>grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em_1.tpr</b></font></p></div></blockquote><br />This is not the line you should be using - you have no flag before "topol.top". However that's also not a problem.<br /><br /><blockquote cite="mid:AANLkTi=f_neVv44JDcoAV+j6J-CAFTCAmd25RvJ5Q-c8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">
<p class="MsoNormal" style="border-width: medium; border-style: none; border-color: -moz-use-text-color; padding: 0in; margin: 0in 0in 0pt;"><font face="Times New Roman" size="3"><font face="Times New Roman">it generates the em_1.tpr file but does not generate any md_out.mdp file and it gives the following 2 notes</font></font></p></div></blockquote><br />Unless you've used "grompp -po md_out.mdp" then the default filename is "mdout.mdp". You need to take care to get all this "punctuation" correct. A few seconds of being careful and methodical can save weeks of pulling out your hair...<br /><br /><blockquote cite="mid:AANLkTi=f_neVv44JDcoAV+j6J-CAFTCAmd25RvJ5Q-c8@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">checking input for internal consistency...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">processing topology...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><b style=""><font size="3"><font face="Times New Roman">NOTE 1 [file topol.top, line 24414]:</font></font></b></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font face="Times New Roman"><span style=""> </span>System has non-zero total charge: 1.400002e+01</font></font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font face="Times New Roman"><span style=""> </span>processing coordinates...</font></font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">double-checking input for internal consistency...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Reading position restraint coords from system_inflated.gro</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">renumbering atomtypes...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">converting bonded parameters...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">initialising group options...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">processing index file...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Analysing residue names:</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Opening library file /usr/local/Gromacs/share/top/aminoacids.dat</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">There are:<span style=""> </span>121<span style=""> </span>OTHER residues</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">There are:<span style=""> </span>408<span style=""> </span>PROTEIN residues</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">There are:<span style=""> </span>0<span style=""> </span>DNA residues</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Analysing Protein...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Analysing Other...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for T-Coupling containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for Acceleration containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for Freeze containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for Energy Mon. containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for VCM containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Number of degrees of freedom in T-Coupling group rest is 29790.00</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for User1 containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for User2 containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for XTC containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for Or. Res. Fit containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Making dummy/rest group for QMMM containing 9931 elements</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Checking consistency between energy and charge groups...</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Calculating fourier grid dimensions for X Y Z</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Using a fourier grid of 216x216x55, spacing 0.119 0.119 0.120</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">Estimate for the relative computational load of the PME mesh part: 0.96</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><b style=""><font size="3"><font face="Times New Roman">NOTE 2 [file aminoacids.dat, line 1]:</font></font></b></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font face="Times New Roman"><span style=""> </span>The optimal PME mesh load for parallel simulations is below 0.5</font></font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font face="Times New Roman"><span style=""> </span>and for highly parallel simulations between 0.25 and 0.33,</font></font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font size="3"><font face="Times New Roman"><span style=""> </span>for higher performance, increase the cut-off and the PME grid spacing</font></font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">This run will generate roughly 116 Mb of data</font></p>
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<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">writing run input file...</font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">There were 2 notes</font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)</font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">------------------------------------------------------------------------------------------</font><font face="Times New Roman" size="3">I understand the note 1 as I haven’t added the ions yet, so the system has charge.</font></p>
<p class="MsoNormal" style="margin: 0in 0in 0pt;"><font face="Times New Roman" size="3">But I am confused about note 2, what changes can I make to .mdp file for the minimization to run smoothly.</font></p></div></blockquote><br />Is the minimization going to run in parallel, or for more than an hour? If not, who cares about parallel performance?<br /><br />Mark