[gmx-users] Using walls and user defined potentials

Olivia Waring owaring at princeton.edu
Mon Nov 28 18:23:45 CET 2011


Hi all,

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:
   wall_atomtype[0]     = 3
   wall_atomtype[1]     = -1
when my input .mdp file said wall_atomtype = wall0.

The log file is shown in full below. Any advice would be greatly
appreciated.

Thanks so much!
Olivia


Input Parameters:
   integrator           = md
   nsteps               = 500000
   init_step            = 0
   ns_type              = Grid
   nstlist              = 5
   ndelta               = 2
   nstcomm              = 10
   comm_mode            = Linear
   nstlog               = 1000
   nstxout              = 1000
   nstvout              = 1000
   nstfout              = 0
   nstcalcenergy        = 5
   nstenergy            = 1000
   nstxtcout            = 1000
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 0
   nky                  = 0
   nkz                  = 0
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xy
   bPeriodicMols        = FALSE
   bContinuation        = TRUE
   bShakeSOR            = FALSE
   etc                  = V-rescale
   nsttcouple           = 5
   epc                  = No
   epctype              = Isotropic
   nstpcouple           = -1
   tau_p                = 2
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   refcoord_scaling     = No
   posres_com (3):
      posres_com[0]= 0.00000e+00
      posres_com[1]= 0.00000e+00
      posres_com[2]= 0.00000e+00
   posres_comB (3):
      posres_comB[0]= 0.00000e+00
      posres_comB[1]= 0.00000e+00
      posres_comB[2]= 0.00000e+00
   andersen_seed        = 815131
   rlist                = 1
   rlistlong            = 1
   rtpi                 = 0.05
   coulombtype          = Cut-off
   rcoulomb_switch      = 0
   rcoulomb             = 1
   vdwtype              = User
   rvdw_switch          = 0
   rvdw                 = 1
   epsilon_r            = 1
   epsilon_rf           = 1
   tabext               = 2
   implicit_solvent     = No
   gb_algorithm         = Still
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 1
   gb_saltconc          = 0
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   gb_dielectric_offset = 0.009
   sa_algorithm         = Ace-approximation
   sa_surface_tension   = 2.05016
   DispCorr             = No
   free_energy          = no
   init_lambda          = 0
   delta_lambda         = 0
   n_foreign_lambda     = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   sc_sigma_min         = 0.3
   nstdhdl              = 10
   separate_dhdl_file   = yes
   dhdl_derivatives     = yes
   dh_hist_size         = 0
   dh_hist_spacing      = 0.1
   nwall                = 1
   wall_type            = table
   wall_atomtype[0]     = 3
   wall_atomtype[1]     = -1
   wall_density[0]      = 0
   wall_density[1]      = 0
   wall_ewald_zfac      = 3
   pull                 = no
   disre                = No
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   dihre-fc             = 1000
   em_stepsize          = 0.01
   em_tol               = 10
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
 userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:         334
   ref_t:         300
   tau_t:         0.1
anneal:          No
ann_npoints:           0
   acc:            0           0           0
   nfreeze:           N           N           N
   energygrp_flags[  0]: 0 0 0 2
   energygrp_flags[  1]: 0 0 0 2
   energygrp_flags[  2]: 0 0 0 2
   energygrp_flags[  3]: 2 2 2 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     TRUE
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
System total charge: 0.000
Read user tables from table.xvg with 1501 data points.
Tabscale = 500 points/nm
Generated table with 1500 data points for COUL.
Tabscale = 500 points/nm
Tabscale = 500 points/nm
Read user tables from table.xvg with 1501 data points.
Tabscale = 500 points/nm
Generated table with 1501 data points for 1-4 COUL.
Tabscale = 500 points/nm
Reading user tables for 3 energy groups with 1 walls
Read user tables from table_CH3_wall0.xvg with 1501 data points.
Tabscale = 500 points/nm
Read user tables from table_CH2_wall0.xvg with 1501 data points.
Tabscale = 500 points/nm
Read user tables from table_S_wall0.xvg with 1501 data points.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.


Initializing LINear Constraint Solver


Started mdrun on node 0 Mon Nov 28 12:02:18 2011

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 5 x 5 x 2 cells
   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    2.63312e+01    7.62753e-01   -2.88371e+03    0.00000e+00    1.63323e+06
   Coulomb (SR)      Potential    Kinetic En.   Total Energy  Conserved En.
    0.00000e+00    1.63037e+06    1.85700e+08    1.87331e+08    1.87331e+08
    Temperature Pressure (bar)   Constr. rmsd
    1.33739e+08    0.00000e+00    7.48703e+00




-- 
Olivia Waring (王维娅)
Princeton University '12
AB Chemistry
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