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<div><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier">Hi<br>I used Gromacs version 3.3.3.<br>My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7<br>)<br>MPI setting =&gt; #PBS -l nodes=4:ppn=4,arch=x86_64   =&gt; 16 nodes in total<br>
After doing the energy minimization, =&gt; the potential energy is extremely<br>high ( say, ten to the 9th order )<br>I visualized the &quot; Simulation-System-EM-solvated.gro &quot; after the energy<br>minimization.<br>Then, I found that the Simulation Sysmtem is devided into 16 domains very<br>
clearly and the molecules (protein, ligand, and water) break into atoms in<br>the boundaries.<br>I have checked that the 20 ligands are not overlapped each other and are not<br>overlapped with protein from the beginning.</span></div>

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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier">More, i have created 10 alike system and each is with &quot;one protein + 20<br>ligand + water molecules&quot;<br>
Two of them get the &quot;minus potential energy&quot; after energy minimization and I<br>can continue running the MD simulation successfully.<br>Others of them get the &quot;extreme high positive potential energy&quot; and the<br>
system is devided into 16 domains after energy minimization and the<br>simulation broke afterall.</span></p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier">With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )<br>There is no problems like that.</span></p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><br>Please give me your ideas to solve the problem.</p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt">The commands are listed below and the .tpr file created by grompp is attached.</p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt">Thank you<br>Lin</p></span>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b><span lang="EN-US" style="COLOR: red"><font face="Times New Roman" size="3"></font></span></b></p><span lang="EN-US"><font face="Times New Roman" size="3">1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top      </font></span><span lang="EN-US"><font face="Times New Roman" size="3">=&gt; G 45a3</font></span> 
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="COLOR: red"><font face="Times New Roman"><font color="#000000"><font size="4">2. Energy minimization of the structure (vacuum)</font></font></font></span></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="4"> </font></span><span lang="EN-US"><font face="Times New Roman" size="3">pbc = no,</font></span></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 14pt; COLOR: red"><font face="Times New Roman"><font color="#000000">3. Periodic boundary conditions</font></font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 7.0 7.0 7.0 </font></span></p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b><span lang="EN-US" style="FONT-SIZE: 14pt; FONT-FAMILY: Courier">4. Add another 20 ligands randomly into the</span></b><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier"> </span><b><span lang="EN-US" style="FONT-SIZE: 14pt; FONT-FAMILY: Courier">simulation (nm^3) box</span></b><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier"></span></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier"><font style="BACKGROUND-COLOR: #ffffff">genbox_mpi -seed 201 -cp 6LYZ-PBC.gro <span style="BACKGROUND: lime">-ci ligand.gro -nmol 2</span>0 -p 6LYZ.top <span style="BACKGROUND: lime">-o 6LYZ20ligand.gro</span></font></span></p>

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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b><span lang="EN-US" style="COLOR: red"><font size="3"><font face="Times New Roman"><font color="#000000">6. Solvent addition</font></font></font></span></b></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3">genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"></p></span></font></span><span lang="EN-US" style="FONT-SIZE: 13pt; BACKGROUND: lime; FONT-FAMILY: Courier"><font style="BACKGROUND-COLOR: #ffffff"><font color="#000000"> </font></font></span><font face="新細明體" size="3"> </font>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b><span lang="EN-US" style="COLOR: red"><font face="Times New Roman"><font color="#000000" size="3">7. Addition of ions: counter charge and concentration</font></font></span></b></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3">grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3">genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL- </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><font color="#000000"></font></p><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier">
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b><span lang="EN-US" style="COLOR: red"><font size="3"><font face="Times New Roman"><font color="#000000">8. Energy minimization of the solvated system</font></font></font></span></b></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="BACKGROUND: yellow"><font size="3"><font face="Times New Roman"><font color="#000000">pbc = xyz (minim.mdp)</font></font></font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3">grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated </font></span><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3"> </font></span></p>

<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" color="#000000" size="3">mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated </font></span></p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"></p></span><font face="新細明體" size="3"> </font></p></div></blockquote></div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)<br>Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)<br>
6LYZ-EM-solvated.tpr:<br>   header:<br>      bIr    = present<br>      bBox   = present<br>      bTop   = present<br>      bX     = present<br>      bV     = present<br>      bF     = not present<br>      natoms = 33042<br>
      step   = 0<br>      t      = 0.000000e+00<br>      lambda = 0.000000e+00<br>   ir:<br>      integrator           = steep<br>      nsteps               = 50000<br>      init_step            = 0<br>      ns_type              = Simple<br>
      nstlist              = 5<br>      ndelta               = 2<br>      bDomDecomp           = FALSE<br>      decomp_dir           = 0<br>      nstcomm              = 1<br>      comm_mode            = Linear<br>      nstcheckpoint        = 1000<br>
      nstlog               = 100<br>      nstxout              = 100<br>      nstvout              = 100<br>      nstfout              = 0<br>      nstenergy            = 1<br>      nstxtcout            = 0<br>      init_t               = 0<br>
      delta_t              = 0.001<br>      xtcprec              = 1000<br>      nkx                  = 0<br>      nky                  = 0<br>      nkz                  = 0<br>      pme_order            = 4<br>      ewald_rtol           = 1e-05<br>
      ewald_geometry       = 0<br>      epsilon_surface      = 0<br>      optimize_fft         = FALSE<br>      ePBC                 = xyz<br>      bUncStart            = FALSE<br>      bShakeSOR            = FALSE<br>      etc                  = No<br>
      epc                  = No<br>      epctype              = Isotropic<br>      tau_p                = 1<br>      ref_p (3x3):<br>         ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>         ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>
         ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>      compress (3x3):<br>         compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>         compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>
         compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>      andersen_seed        = 815131<br>      rlist                = 1<br>      coulombtype          = Cut-off<br>      rcoulomb_switch      = 0<br>      rcoulomb             = 1<br>
      vdwtype              = Cut-off<br>      rvdw_switch          = 0<br>      rvdw                 = 1<br>      epsilon_r            = 1<br>      epsilon_rf           = 1<br>      tabext               = 1<br>      gb_algorithm         = Still<br>
      nstgbradii           = 1<br>      rgbradii             = 2<br>      gb_saltconc          = 0<br>      implicit_solvent     = No<br>      DispCorr             = No<br>      fudgeQQ              = 1<br>      free_energy          = no<br>
      init_lambda          = 0<br>      sc_alpha             = 0<br>      sc_power             = 0<br>      sc_sigma             = 0.3<br>      delta_lambda         = 0<br>      disre_weighting      = Conservative<br>      disre_mixed          = FALSE<br>
      dr_fc                = 1000<br>      dr_tau               = 0<br>      nstdisreout          = 100<br>      orires_fc            = 0<br>      orires_tau           = 0<br>      nstorireout          = 100<br>      dihre-fc             = 1000<br>
      dihre-tau            = 0<br>      nstdihreout          = 100<br>      em_stepsize          = 0.01<br>      em_tol               = 1<br>      niter                = 20<br>      fc_stepsize          = 0<br>      nstcgsteep           = 1000<br>
      nbfgscorr            = 10<br>      ConstAlg             = Lincs<br>      shake_tol            = 0.0001<br>      lincs_order          = 4<br>      lincs_warnangle      = 30<br>      lincs_iter           = 1<br>      bd_fric              = 0<br>
      ld_seed              = 1993<br>      cos_accel            = 0<br>      deform (3x3):<br>         deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>         deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>
         deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>      userint1             = 0<br>      userint2             = 0<br>      userint3             = 0<br>      userint4             = 0<br>      userreal1            = 0<br>
      userreal2            = 0<br>      userreal3            = 0<br>      userreal4            = 0<br>grpopts:<br>      nrdf:            99123<br>      ref_t:               0<br>      tau_t:               0<br>anneal:                   No<br>
ann_npoints:               0<br>      acc:                 0           0           0<br>      nfreeze:           N           N           N<br>      energygrp_flags[  0]: 0<br>      efield-x:<br>         n = 0<br>      efield-xt:<br>
         n = 0<br>      efield-y:<br>         n = 0<br>      efield-yt:<br>         n = 0<br>      efield-z:<br>         n = 0<br>      efield-zt:<br>         n = 0<br>      bQMMM                = FALSE<br>      QMconstraints        = 0<br>
      QMMMscheme           = 0<br>      scalefactor          = 1<br>qm_opts:<br>      ngQM                 = 0<br>   box (3x3):<br>      box[    0]={ 7.00000e+00,  0.00000e+00,  0.00000e+00}<br>      box[    1]={ 0.00000e+00,  7.00000e+00,  0.00000e+00}<br>
      box[    2]={ 0.00000e+00,  0.00000e+00,  7.00000e+00}<br>   boxv (3x3):<br>      boxv[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>      boxv[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>      boxv[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br>
   pcoupl_mu (3x3):<br>      pcoupl_mu[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}<br>      pcoupl_mu[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}<br>      pcoupl_mu[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}<br>
   nosehoover_xi:                  0<br>   x (33042x3):<br>      x[    0]={ 3.88200e+00,  2.44200e+00,  2.61100e+00}<br>      x[    1]={ 3.87900e+00,  2.34300e+00,  2.62700e+00}<br>      x[    2]={ 3.97600e+00,  2.47000e+00,  2.59300e+00}<br>
      x[    3]={ 3.85000e+00,  2.49000e+00,  2.69300e+00}<br>      x[    4]={ 3.79500e+00,  2.47800e+00,  2.49600e+00}<br>      x[    5]={ 3.65000e+00,  2.43700e+00,  2.52700e+00}<br>      x[    6]={ 3.55300e+00,  2.46400e+00,  2.41200e+00}<br>
      x[    7]={ 3.41000e+00,  2.42200e+00,  2.44600e+00}<br></blockquote></div>