David Waroquiers wrote:
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.
It's vanishingly rare for GROMACS to segfault without an error message.
Consult all of stdout, stderr and your .log file for messages.
Probably, your combination of starting configuration and model physics
are broken. If you're confident your starting configuration is good
(e.g. you know it works with some other Si-O force field) then you'll
have to go over your table files, I suppose.
Mark
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
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
