On 11/6/13 12:53 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I have simulated ionomer in water solution using gromos force field. But in
middle of simulation(after 2 ns) the simulation stopped and I received these
messages:
WARNING: Listed nonbonded interaction between particles 174 and 188
at distance 3f which is larger than the table limit 3f nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Fatal error:
1 particles communicated to PME node 5 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
----
I used simulated annealing for equilibrating the system in NVT and NPT
condition. The mdp files are:
---- NVT ------
define = -DPOSRES
integrator = md
dt = 0.002 ; time step (in ps)
nsteps = 25000 ; Maximum number of steps to perform
; OUTPUT CONTROL OPTIONS
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500
energygrps = Non-Water Water
; NEIGHBORSEARCHING PARAMETERS
nstlist = 1
ns_type = grid
rlist = 1.5
pbc = xyz
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype= PME
pme_order = 4
fourierspacing= 0.16
rcoulomb = 1.5
vdw-type = Cut-off
rvdw = 1.5
; Temperature coupling
tcoupl = v-rescale
tc-grps = Non-Water Water
tau_t = 0.1 0.1
ref_t = 300 300
; Dispersion correction
DispCorr = EnerPres
; Pressure coupling is off
pcoupl = no
; Annealing
annealing = single single
annealing-npoints = 5 5
annealing-time = 0 10 20 30 40 0 10 20 30 40
annealing-temp = 300 320 340 360 380 300 320 340 360 380
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS
constraints = ; all-bonds
continuation= no
constraint_algorithm = lincs
lincs_iter = 1
lincs_order= 4
--------- NPT ------------
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 25000
; OUTPUT CONTROL OPTIONS
nstxout = 500
nstvout = 500
nstfout = 500
nstenergy = 500
nstlog = 500
energygrps = Non-Water Water
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5
ns_type = grid
rlist = 1.5
pbc = xyz
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype= PME
pme_order = 4
fourierspacing= 0.16
rcoulomb = 1.5
vdw-type = Cut-off
rvdw = 1.5
; Temperature coupling
tcoupl = v-rescale
tc-grps = Non-Water Water
tau_t = 0.1 0.1
ref_t = 300 300
; Dispersion correction
DispCorr = EnerPres
pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
; Annealing
annealing = single single
annealing-npoints = 5 5
annealing-time = 0 10 20 30 40 0 10 20 30 40
annealing-temp = 380 360 340 320 300 380 360 340 320 300
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
; OPTIONS FOR BONDS
constraints = ; all-bonds
continuation= yes ;continuation from NVT
constraint_algorithm = lincs
lincs_iter = 1
lincs_order= 4
--------------------------
Is the equilibration time is long enough? I appreciate any help/suggestion
regarding my case.
The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets.
Likely the dynamics have become unstable due to violation of the physical model.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
