GROMACS version:2019.4
GROMACS modification: no
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Hi All
I am trying to simulate the CG-MD simulation using user-defined tables (Developed using VOTCA). When I am trying to run the simulation I am getting the following error:
Fatal error:
A tabulated bond interaction table number 1 is out of the table range: r
2.510880, between table indices 1255 and 1256, table length 1251
My CG system contains 1200 beads.
my topology file is :
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 0.0 0.0
[ atomtypes ]
;type mass charge ptype sigma epsilon
BC 75.00000 0.354939 A 1.000000000 1.000000000
IM 86.00000 0.858969 A 1.000000000 1.000000000
FB 82.00000 -1.000000 A 1.000000000 1.000000000
[ moleculetype ]
; Name nrexcl
B1I 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 BC 1 B1I BCZ 1 0.354939 75.0000000 ; qtot 0
2 IM 1 B1I I1M 2 0.858969 86.0000000 ; qtot 0
3 IM 1 B1I I2M 3 0.949364 86.0000000 ; qtot 0
4 IM 1 B1I I3M 4 0.836728 86.0000000 ; qtot 3
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 8 1 1.0
1 3 8 1 1.0
1 4 8 1 1.0
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 8 1 1.0
2 1 4 8 1 1.0
3 1 4 8 1 1.0
[ moleculetype ]
; Name nrexcl
BF4 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 FB 1 BF4 FB 1 -1.00000 82.0000000 ; qtot 0
[ system ]
cg B1I BF4
[ molecules ]
; Compound #mols
B1I 300
BF4 900
My MDP file is
; VARIOUS PREPROCESSING OPTIONS
title = NVT simulation (constant number, volume and temperature)
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.005
nsteps = 400000
cutoff-scheme = group
; OUTPUT CONTROL OPTIONS
nstxout = 2500 ; (coordinates)
nstvout = 2500 ; (velocities)
nstfout = 0 ; No output, except for last frame (forces)
nstlog = 2500 ; Write every step to the log
nstenergy = 2500 ; Write energies at every step
nstxtcout = 2500 ; Do not write a compressed trajectory
energygrps = BC IM FB ; Write energy information separately for these groups
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.5
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = User
pme_order = 4
fourierspacing = 0.16
vdw-type = User
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table = BC BC IM IM FB FB BC IM BC FB IM FB
; Temperature coupling
tcoupl = berendsen
tc-grps = BC IM FB
tau_t = 0.5 0.5 0.5
ref_t = 300 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = Isotropic
tau_p = 2
compressibility = 4.5e-5
ref_p = 1.0
DispCorr = EnerPres
refcoord_scaling = com
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = -1
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = lincs
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
I have seen simulation is running if I use very small time step dt = 0.0005, while this does will not run slightly higher time step in only NVT and NPT.
Can you please help in solving this issue. Any suggestions in running the simulations without this or any further error? would also helpful.
Thank you in Advance.
Praveen