[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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