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<P><FONT face="Courier New, Courier, Monospace">Hi everybody!</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">I am new in modelling and working on a membrane proteine. I made a hole with the package mdrun_make_hole in a POPE bilayer and i embed my proteine in. then I used genbox and genion to put it in NaCl solvent. Then i was thinking i had to do an energy minimisation with the steepest descent. The problem is that my potential energy don't move at all and stay very big. Does that mean that My hole is bad and i have to do it again with an other probe size for exemple? or am I completly wrong on the simulation method and there is something else to do on the different component?</FONT></P>
<P><FONT face="Courier New">here is th .log result:</FONT></P><FONT size=2>
<P><FONT face="Courier New, Courier, Monospace">There are 0 atoms for free energy perturbation</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Input Parameters:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">integrator = steep</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsteps = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ns_type = Grid</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstlist = 5</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ndelta = 2</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bDomDecomp = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">decomp_dir = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstcomm = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstlog = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstxout = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstvout = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstfout = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstenergy = 50</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstxtcout = 50</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">init_t = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">delta_t = 0.001</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">xtcprec = 1000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nkx = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nky = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nkz = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">pme_order = 4</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ewald_rtol = 1e-05</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ewald_geometry = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">epsilon_surface = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">optimize_fft = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ePBC = xyz</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bUncStart = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bShakeSOR = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">etc = No</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">epc = No</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">epctype = Isotropic</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">tau_p = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_p (3x3):</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">compress (3x3):</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bSimAnn = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">zero_temp_time = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rlist = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">coulombtype = Cut-off</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rcoulomb_switch = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rcoulomb = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">vdwtype = Cut-off</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rvdw_switch = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rvdw = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">epsilon_r = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">DispCorr = No</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">fudgeQQ = 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">free_energy = no</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">init_lambda = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">sc_alpha = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">sc_sigma = 0.3</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">delta_lambda = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">disre_weighting = Conservative</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">disre_mixed = FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">dr_fc = 1000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">dr_tau = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstdisreout = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">orires_fc = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">orires_tau = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstorireout = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">em_stepsize = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">em_tol = 2000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">niter = 20</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">fc_stepsize = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstcgsteep = 1000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ConstAlg = Lincs</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">shake_tol = 0.0001</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">lincs_order = 4</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">lincs_warnangle = 30</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bd_temp = 300</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">bd_fric = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ld_seed = 1993</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">cos_accel = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userint1 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userint2 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userint3 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userint4 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userreal1 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userreal2 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userreal3 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">userreal4 = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">grpopts:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nrdf: 838185</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_t: 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">tau_t: 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">acc: 0 0 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nfreeze: N N N</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">energygrp_excl[ 0]: 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-x:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-xt:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-y:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-yt:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-z:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">efield-zt:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">n = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">CPU= 0, lastcg=102020, targetcg=51010, myshift= 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->shift = 1, nsb->bshift= 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Neighbor Search Blocks</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->nodeid: 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->nnodes: 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->cgtotal: 102021</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->natoms: 279396</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->shift: 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsb->bshift: 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Nodeid index homenr cgload workload</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">0 0 279396 102021 102021</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Max number of bonds per atom is 4</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Table routines are used for coulomb: FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Table routines are used for vdw: FALSE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Cut-off's: NS: 1 Coulomb: 1 LJ: 1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Generated table with 500 data points for COUL.</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Tabscale = 500 points/nm</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Generated table with 500 data points for LJ6.</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Tabscale = 500 points/nm</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Generated table with 500 data points for LJ12.</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Tabscale = 500 points/nm</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Going to determine what solvent types we have.</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">There are 85086 molecules, 102021 charge groups and 279396 atoms</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">There are 0 optimized solvent molecules on node 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">There are 84303 optimized water molecules on node 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Initiating Steepest Descents</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Center of mass motion removal mode is Linear</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">We have the following groups for center of mass motion removal:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">0: rest, initial mass: 1.8663e+06</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Started Steepest Descents on node 0 Sat Jan 4 10:08:56 2003</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Removing pbc first time</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Done rmpbc</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Steepest Descents:</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Tolerance = 2.00000e+03</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Number of steps = 100</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Grid: 26 x 26 x 36 cells</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Step Time Lambda Annealing</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">0 0.00000 0.00000 0.00000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">...</FONT></P><FONT size=2>
<P><FONT face="Courier New, Courier, Monospace">Stepsize too small (7.45058e-07 nm)Converged to machine precision,</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">but not to the requested precision (2000)</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Steepest Descents did not converge in 28 steps</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Potential Energy = 5.89591e+19</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Maximum force: inf</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">M E G A - F L O P S A C C O U N T I N G</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">RF=Reaction-field Free=Free Energy SC=Softcore</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">T=Tabulated S=Solvent W=Water WW=Water-Water</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Computing: M-Number M-Flop's % Flop's</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">LJ 52.971884 1642.128404 2.9</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Coulomb 56.221032 1517.967864 2.6</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Coulomb(W) 311.138632 25202.229192 43.8</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">LJ + Coulomb 42.337988 1608.843544 2.8</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">LJ + Coul(W) 161.822332 14887.654544 25.9</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Innerloop-Iatom 20.991432 209.914320 0.4</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">NS-Pairs 537.598208 11289.562368 19.6</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Reset In Box 7.823088 70.407792 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Shift-X 7.810096 46.860576 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">CG-CoM 2.856588 82.841052 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Bonds 5.444852 234.128636 0.4</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Angles 3.278828 534.448964 0.9</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Propers 0.366436 83.913844 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Impropers 0.170100 35.380800 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">RB-Dihedrals 0.204792 50.583624 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Virial 0.000756 0.013608 0.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Total 57496.87913 100.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">NODE (s) Real (s) (%)</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Time: 333.000 333.000 100.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">5:33</FONT></P></FONT></FONT>
<P><FONT face="Courier New">Or is it possible that my protein and my bilayer where not enough good before I used them? How to know?</FONT></P>
<P><FONT face="Courier New">I tryed to calculate single point but i got segmentation fault I must be wrong in parameters:</FONT></P><FONT size=2>
<P><FONT face="Courier New, Courier, Monospace">title = POPE</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">cpp = /lib/cpp</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">constraints = all-bonds</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">integrator = md</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">dt = 0.002</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nsteps = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstcomm = 1</FONT></P>
<P><FONT face="Courier New"></FONT><FONT size=2></FONT><FONT face="Courier New, Courier, Monospace">nstxout = 50</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstvout = 1000</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstfout = 0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstlog = 10</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstenergy = 10</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">nstlist = 10</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ns_type = grid</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rlist = 1.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rcoulomb = 1.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">rvdw = 1.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Tcoupl = Berendsen</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">tc-grps = System</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">tau_t = 0.1</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_t = 300 </FONT></P>
<P><FONT face="Courier New, Courier, Monospace">energygrps = System</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Pcoupl = Berendsen</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">Pcoupltype = Anisotropic </FONT></P>
<P><FONT face="Courier New, Courier, Monospace">tau_P = 1.0 1.0 1.0 1.0 1.0 1.0 </FONT></P>
<P><FONT face="Courier New, Courier, Monospace">compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">ref_p = 1.0 1.0 1.0 1.0 1.0 1.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">gen_vel = yes</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">gen_temp = 300.0</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">gen_seed = 173529</FONT></P></FONT>
<P><BR> </P>
<P><FONT face="Courier New">here is when the error segmentation happen:</FONT></P><FONT size=2>
<P>.log:</P>
<P>...</P>
<P>Initializing LINear Constraint Solver</P>
<P>number of constraints is 25853</P>
<P>average number of constraints coupled to one constraint is 2.5</P>
<P><FONT face="Courier New, Courier, Monospace">a little help would really be welcome as i feel really lost at the moment.</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">thanks,</FONT></P>
<P><FONT face="Courier New, Courier, Monospace">audrey</FONT></FONT><BR><BR></P>
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<DIV><STRONG><FONT face="Courier New, Courier, Monospace" color=#ff6633></DIV>
<HR>
<DIV></DIV>Herr Audrey </FONT></STRONG>
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<DIV><STRONG><FONT face="Courier New, Courier, Monospace" color=#ff6633><FONT color=#3333cc>exchange student in Bioinformatics and modelling</FONT> </FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#ff6633>0416 363 076</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#ff6633></FONT></STRONG> </DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>University of Sydney 425 Harris St.</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>physical chemestry Ultimo, Sydney 2007</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>(+61)02 9036 9151 (+61)02 9660 6991</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399></FONT></STRONG> </DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>ou en France:</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>6 alle des cytises</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>71640 Dracy le Fort</FONT></STRONG></DIV>
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