Hi all,<div><br></div><div>I am simulating a self-assembled monolayer of alkanethiols under the influence of a 12-3 surface potential. I have been trying to implement this potential function using the "walls" and "tables" features of GROMACS. There are four atom types in my system: CH3, CH2, S, and wall0. The following three interaction types - CH3 + wall0, CH2 + wall0, and S + wall0 - are governed by tables that I provided. All other interaction types are taken care of by a default table.xvg file (which corresponds to a standard LJ potential). My production runs are crashing, and I'm really not sure why, although my first guess is that it might have something to do with the wall_r_linpot value. I'm also not sure why the log file has the following two entries:Â </div>
<div>  wall_atomtype[0]   = 3</div><div>  wall_atomtype[1]   = -1</div><div>when my input .mdp file said wall_atomtype = wall0. </div><div><br></div><div>The log file is shown in full below. Any advice would be greatly appreciated. </div>
<div><br></div><div>Thanks so much!</div><div>Olivia</div><div><br></div><div><br></div><div><div>Input Parameters:</div><div>  integrator      = md</div><div>  nsteps        = 500000</div><div>  init_step       = 0</div>
<div>  ns_type        = Grid</div><div>  nstlist        = 5</div><div>  ndelta        = 2</div><div>  nstcomm        = 10</div><div>  comm_mode       = Linear</div><div>  nstlog        = 1000</div>
<div>  nstxout        = 1000</div><div>  nstvout        = 1000</div><div>  nstfout        = 0</div><div>  nstcalcenergy     = 5</div><div>  nstenergy       = 1000</div><div>  nstxtcout       = 1000</div>
<div>  init_t        = 0</div><div>  delta_t        = 0.002</div><div>  xtcprec        = 1000</div><div>  nkx          = 0</div><div>  nky          = 0</div><div>  nkz          = 0</div>
<div>  pme_order       = 4</div><div>  ewald_rtol      = 1e-05</div><div>  ewald_geometry    = 0</div><div>  epsilon_surface    = 0</div><div>  optimize_fft     = FALSE</div><div>  ePBC         = xy</div>
<div>  bPeriodicMols     = FALSE</div><div>  bContinuation     = TRUE</div><div>  bShakeSOR       = FALSE</div><div>  etc          = V-rescale</div><div>  nsttcouple      = 5</div><div>  epc          = No</div>
<div>  epctype        = Isotropic</div><div>  nstpcouple      = -1</div><div>  tau_p         = 2</div><div>  ref_p (3x3):</div><div>   ref_p[   0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}</div>
<div>Â Â Â ref_p[ Â Â 1]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div><div>Â Â Â ref_p[ Â Â 2]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div><div>Â Â compress (3x3):</div><div>Â Â Â compress[ Â Â 0]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div>
<div>   compress[   1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}</div><div>   compress[   2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}</div><div>  refcoord_scaling   = No</div><div>  posres_com (3):</div><div>
   posres_com[0]= 0.00000e+00</div><div>   posres_com[1]= 0.00000e+00</div><div>   posres_com[2]= 0.00000e+00</div><div>  posres_comB (3):</div><div>   posres_comB[0]= 0.00000e+00</div><div>   posres_comB[1]= 0.00000e+00</div>
<div>   posres_comB[2]= 0.00000e+00</div><div>  andersen_seed     = 815131</div><div>  rlist         = 1</div><div>  rlistlong       = 1</div><div>  rtpi         = 0.05</div><div>  coulombtype      = Cut-off</div>
<div>  rcoulomb_switch    = 0</div><div>  rcoulomb       = 1</div><div>  vdwtype        = User</div><div>  rvdw_switch      = 0</div><div>  rvdw         = 1</div><div>  epsilon_r       = 1</div>
<div>  epsilon_rf      = 1</div><div>  tabext        = 2</div><div>  implicit_solvent   = No</div><div>  gb_algorithm     = Still</div><div>  gb_epsilon_solvent  = 80</div><div>  nstgbradii      = 1</div>
<div>  rgbradii       = 1</div><div>  gb_saltconc      = 0</div><div>  gb_obc_alpha     = 1</div><div>  gb_obc_beta      = 0.8</div><div>  gb_obc_gamma     = 4.85</div><div>  gb_dielectric_offset = 0.009</div>
<div>  sa_algorithm     = Ace-approximation</div><div>  sa_surface_tension  = 2.05016</div><div>  DispCorr       = No</div><div>  free_energy      = no</div><div>  init_lambda      = 0</div><div>  delta_lambda     = 0</div>
<div>  n_foreign_lambda   = 0</div><div>  sc_alpha       = 0</div><div>  sc_power       = 0</div><div>  sc_sigma       = 0.3</div><div>  sc_sigma_min     = 0.3</div><div>  nstdhdl        = 10</div>
<div>  separate_dhdl_file  = yes</div><div>  dhdl_derivatives   = yes</div><div>  dh_hist_size     = 0</div><div>  dh_hist_spacing    = 0.1</div><div>  nwall         = 1</div><div>  wall_type       = table</div>
<div>  wall_atomtype[0]   = 3</div><div>  wall_atomtype[1]   = -1</div><div>  wall_density[0]    = 0</div><div>  wall_density[1]    = 0</div><div>  wall_ewald_zfac    = 3</div><div>  pull         = no</div>
<div>  disre         = No</div><div>  disre_weighting    = Conservative</div><div>  disre_mixed      = FALSE</div><div>  dr_fc         = 1000</div><div>  dr_tau        = 0</div><div>  nstdisreout      = 100</div>
<div>  orires_fc       = 0</div><div>  orires_tau      = 0</div><div>  nstorireout      = 100</div><div>  dihre-fc       = 1000</div><div>  em_stepsize      = 0.01</div><div>  em_tol        = 10</div>
<div>  niter         = 20</div><div>  fc_stepsize      = 0</div><div>  nstcgsteep      = 1000</div><div>  nbfgscorr       = 10</div><div>  ConstAlg       = Lincs</div><div>  shake_tol       = 0.0001</div>
<div>  lincs_order      = 4</div><div>  lincs_warnangle    = 30</div><div>  lincs_iter      = 1</div><div>  bd_fric        = 0</div><div>  ld_seed        = 1993</div><div>  cos_accel       = 0</div>
<div>Â Â deform (3x3):</div><div>Â Â Â deform[ Â Â 0]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div><div>Â Â Â deform[ Â Â 1]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div><div>Â Â Â deform[ Â Â 2]={ 0.00000e+00, Â 0.00000e+00, Â 0.00000e+00}</div>
<div>Â Â userint1 Â Â Â Â Â Â = 0</div><div>Â Â userint2 Â Â Â Â Â Â = 0</div><div>Â userint3 Â Â Â Â Â Â = 0</div><div>Â Â userint4 Â Â Â Â Â Â = 0</div><div>Â Â userreal1 Â Â Â Â Â Â = 0</div><div>Â Â userreal2 Â Â Â Â Â Â = 0</div>
<div>Â Â userreal3 Â Â Â Â Â Â = 0</div><div>Â Â userreal4 Â Â Â Â Â Â = 0</div><div>grpopts:</div><div>Â Â nrdf: Â Â Â Â 334</div><div>Â Â ref_t: Â Â Â Â 300</div><div>Â Â tau_t: Â Â Â Â 0.1</div><div>anneal: Â Â Â Â Â No</div><div>
ann_npoints: Â Â Â Â Â 0</div><div>Â Â acc: Â Â Â Â Â Â 0 Â Â Â Â Â 0 Â Â Â Â Â 0</div><div>Â Â nfreeze: Â Â Â Â Â N Â Â Â Â Â N Â Â Â Â Â N</div><div>Â Â energygrp_flags[ Â 0]: 0 0 0 2</div><div>Â Â energygrp_flags[ Â 1]: 0 0 0 2</div>
<div>Â Â energygrp_flags[ Â 2]: 0 0 0 2</div><div>Â Â energygrp_flags[ Â 3]: 2 2 2 0</div><div>Â Â efield-x:</div><div>Â Â Â n = 0</div><div>Â Â efield-xt:</div><div>Â Â Â n = 0</div><div>Â Â efield-y:</div><div>Â Â Â n = 0</div>
<div>  efield-yt:</div><div>   n = 0</div><div>  efield-z:</div><div>   n = 0</div><div>  efield-zt:</div><div>   n = 0</div><div>  bQMMM         = FALSE</div><div>  QMconstraints     = 0</div><div>
  QMMMscheme      = 0</div><div>  scalefactor      = 1</div><div>qm_opts:</div><div>  ngQM         = 0</div><div>Table routines are used for coulomb: FALSE</div><div>Table routines are used for vdw:   TRUE</div>
<div>Cut-off's: Â NS: 1 Â Coulomb: 1 Â LJ: 1</div><div>System total charge: 0.000</div><div>Read user tables from table.xvg with 1501 data points.</div><div>Tabscale = 500 points/nm</div><div>Generated table with 1500 data points for COUL.</div>
<div>Tabscale = 500 points/nm</div><div>Tabscale = 500 points/nm</div><div>Read user tables from table.xvg with 1501 data points.</div><div>Tabscale = 500 points/nm</div><div>Generated table with 1501 data points for 1-4 COUL.</div>
<div>Tabscale = 500 points/nm</div><div>Reading user tables for 3 energy groups with 1 walls</div><div>Read user tables from table_CH3_wall0.xvg with 1501 data points.</div><div>Tabscale = 500 points/nm</div><div>Read user tables from table_CH2_wall0.xvg with 1501 data points.</div>
<div>Tabscale = 500 points/nm</div><div>Read user tables from table_S_wall0.xvg with 1501 data points.</div><div>Tabscale = 500 points/nm</div><div>Configuring nonbonded kernels...</div><div>Configuring standard C nonbonded kernels...</div>
<div>Testing x86_64 SSE2 support... present.</div><div><br></div><div><br></div><div>Initializing LINear Constraint Solver</div><div><br></div><div><br></div><div>Started mdrun on node 0 Mon Nov 28 12:02:18 2011</div><div>
<br></div><div>      Step      Time     Lambda</div><div>       0     0.00000     0.00000</div><div><br></div><div>Grid: 5 x 5 x 2 cells</div><div>  Energies (kJ/mol)</div><div>     Angle Ryckaert-Bell.      LJ-14   Coulomb-14     LJ (SR)</div>
<div>  2.63312e+01   7.62753e-01  -2.88371e+03   0.00000e+00   1.63323e+06</div><div>  Coulomb (SR)    Potential   Kinetic En.  Total Energy  Conserved En.</div><div>  0.00000e+00   1.63037e+06   1.85700e+08   1.87331e+08   1.87331e+08</div>
<div>  Temperature Pressure (bar)  Constr. rmsd</div><div>  1.33739e+08   0.00000e+00   7.48703e+00</div></div><div><br></div><div><br><br clear="all"><div><br></div>-- <br><div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div><br>
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