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: </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> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> compress (3x3):</div><div> compress[ 0]={ 0.00000e+00, 0.00000e+00, 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> deform (3x3):</div><div> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div>
<div> userint1 = 0</div><div> userint2 = 0</div><div> userint3 = 0</div><div> userint4 = 0</div><div> userreal1 = 0</div><div> userreal2 = 0</div>
<div> userreal3 = 0</div><div> userreal4 = 0</div><div>grpopts:</div><div> nrdf: 334</div><div> ref_t: 300</div><div> tau_t: 0.1</div><div>anneal: No</div><div>
ann_npoints: 0</div><div> acc: 0 0 0</div><div> nfreeze: N N N</div><div> energygrp_flags[ 0]: 0 0 0 2</div><div> energygrp_flags[ 1]: 0 0 0 2</div>
<div> energygrp_flags[ 2]: 0 0 0 2</div><div> energygrp_flags[ 3]: 2 2 2 0</div><div> efield-x:</div><div> n = 0</div><div> efield-xt:</div><div> n = 0</div><div> efield-y:</div><div> 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: NS: 1 Coulomb: 1 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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