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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 => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total<br>
After doing the energy minimization, => the potential energy is extremely<br>high ( say, ten to the 9th order )<br>I visualized the " Simulation-System-EM-solvated.gro " 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 "one protein + 20<br>ligand + water molecules"<br>
Two of them get the "minus potential energy" after energy minimization and I<br>can continue running the MD simulation successfully.<br>Others of them get the "extreme high positive potential energy" 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">=> 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>
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<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>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier"><font style="BACKGROUND-COLOR: #ffffff"><span style="BACKGROUND: lime"></span></font></span> </p><span lang="EN-US" style="FONT-SIZE: 13pt; FONT-FAMILY: Courier"><font style="BACKGROUND-COLOR: #ffffff"><span style="BACKGROUND: lime">
<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>
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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>
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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">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>