[gmx-users] Problem with user-defined potentials

[David Waroquiers]

Hello,

I'm getting problems to simulate amorphous silica with potentials I made
myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg
(which should not be used as all the possible non-bonded interactions
are given in the three previous tables).

The generation of the topology file with grompp works well but when I'm
try to simulate my system (mdrun), Im getting a segmentation fault. Am I
missing something in the topology file or grompp.mdp file ? I just want
to have the non-bonded interactions defined in my tables to be applied.
My topology and input file are hereafter. I can give you my tables.xvg
but they are too big to be posted on the forum.

Thanks a lot

My topology file TOPOL.TOP is the following :

[ defaults ]
 2 1 0
[ atomtypes ]
; name      mass   charge       ptype           c6            c12
 O      15.99940     -0.955209      A           1.0           1.0
0.0000;
 Si     28.08550      1.910418      A           1.0           1.0
0.0000;
[ nonbond_params ]
  O       O      2      1       1       1
  O      Si      2      1       1       1
  Si     Si      2      1       1       1
[ moleculetype ]
 O      0
[ atoms ]
 1       O      1       O        O      1       -0.955209     15.99940
[ moleculetype ]
 Si     0;
[ atoms ]
 1       Si     1       Si      Si      2        1.910418     28.08550
[ system ]
 Silica
[ molecules ]
O        384
Si       192

and my mdrun input file GROMPP.MDP is :

 title                   = 576-atoms a-SiO2 model 01
 cpp                     = cpp
 define                  =
 integrator              = md
 dt                      = 0.001
 nsteps                  = 25000

; Coulomb type

 coulombtype             = User
 vdwtype                 = User
 rvdw                    = 1.0
 rlist                   = 1.0
 rcoulomb                = 1.0
 fourierspacing          = 0.1
 ewald_rtol              = 1e-5
 energygrps              = Si O
 energygrp_table         = Si Si Si O O O

; Temperature Coupling

 tcoupl                  = nose-hoover
 tc_grps                 = System
 tau_t                   = 0.02
 ref_t                   = 7000
 gen_vel                 = yes
 gen_temp                = 7000
 gen_seed                = -1

; Simulated Annealing

; annealing               = single
; annealing_npoints       = 3
; annealing_time          = 0 56 150
; annealing_temp          = 5000 5000 300

; Output parameters

 nstxout                 = 100
 nstxtcout               = 1000

-- 
-----------------------------------------------------------
David Waroquiers, Phd Student
European Theoretical Spectroscopy Facility (ETSF)
Unité de Physico-Chimie et de Physique des Matériaux (PCPM)
Université Catholique de Louvain (UCL)
-----------------------------------------------------------
Address :
Bâtiment Boltzmann
Place Croix du Sud, 1
1348 Louvain-la-Neuve, Belgique
-----------------------------------------------------------
E-mail : david.waroquiers at uclouvain.be
Tel : + 32 (0)10 / 47 28 38
Fax : + 32 (0)10 / 47 34 52
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