[gmx-users] error in the middle of running mdrun_mpi

[Nizar Masbukhin]

Thanks for yor reply, Mark.


At first i was sure that the problem was table-exension because when I
enlarge table-extension value, warning message didn't  appear anymore.
Besides, i have successfully minimized and equilibrated the system
(indicated by Fmax < emtol reached; and no error messages during NVT&NPT
equilibration, except a warning that the Pcouple is turned off in vacuum
system).

However, the error message appeared without table-extension warning makes
me doubt also about my system stability. Here is my mdp setting. Please
tell me if there are any 'weird' setting, and also kindly suggest/recommend
a better setting.


*mdp file for Minimisation*

integrator = steep

nsteps = 5000

emtol = 200

emstep = 0.01

niter = 20

nstlog = 1

nstenergy = 1

cutoff-scheme = group

nstlist = 1

ns_type = simple

pbc = no

rlist = 0.5

coulombtype = cut-off

rcoulomb = 0.5

vdw-type = cut-off

rvdw-switch = 0.8

rvdw = 0.5

DispCorr = no

fourierspacing = 0.12

pme_order = 6

ewald_rtol = 1e-06

epsilon_surface = 0

optimize_fft = no

tcoupl = no

pcoupl = no

free_energy = yes

init_lambda = 0.0

delta_lambda = 0

foreign_lambda = 0.05

sc-alpha = 0.5

sc-power = 1.0

sc-sigma  = 0.3

couple-lambda0 = vdw

couple-lambda1 = none

couple-intramol = no

nstdhdl = 10

gen_vel = no

constraints = none

constraint-algorithm = lincs

continuation = no

lincs-order  = 12

implicit-solvent = GBSA

gb-algorithm = still

nstgbradii = 1

rgbradii = 0.5

gb-epsilon-solvent = 80

sa-algorithm = Ace-approximation

sa-surface-tension = 2.05


*mdp file for NVT equilibration*

define = -DPOSRES

integrator = md

tinit = 0

dt = 0.002

nsteps = 250000

init-step = 0

comm-mode = angular

nstcomm = 100

bd-fric = 0

ld-seed = -1

nstxout = 1000

nstvout = 50000

nstfout = 50000

nstlog = 100

nstcalcenergy = 100

nstenergy = 1000

nstxtcout = 100

xtc-precision = 1000

xtc-grps = system

energygrps = system

cutoff-scheme= group

nstlist                  = 1

ns-type = simple

pbc= no

rlist= 0.5

coulombtype = cut-off

rcoulomb= 0.5

vdw-type = Cut-off

vdw-modifier = Potential-shift-Verlet

rvdw-switch= 0.8

rvdw = 0.5

table-extension = 500

fourierspacing = 0.12

fourier-nx  = 0

fourier-ny = 0

fourier-nz = 0

implicit-solvent = GBSA

gb-algorithm = still

nstgbradii = 1

rgbradii = 0.5

gb-epsilon-solvent = 80

sa-algorithm = Ace-approximation

sa-surface-tension = 2.05

tcoupl = v-rescale

nsttcouple = -1

nh-chain-length = 10

print-nose-hoover-chain-variables = no

tc-grps = system

tau-t = 0.1

ref-t = 298.00

pcoupl = No

pcoupltype = Isotropic

nstpcouple = -1

tau-p = 1

refcoord-scaling = No

gen-vel = yes

gen-temp = 298.00

gen-seed  = -1

constraints= all-bonds

constraint-algorithm = Lincs

continuation = no

Shake-SOR = no

shake-tol = 0.0001

lincs-order = 4

lincs-iter = 1

lincs-warnangle = 30


*mdp file for NPT equilibration*

define = -DPOSRES

integrator = md

tinit = 0

dt = 0.002

nsteps = 500000

init-step = 0

simulation-part = 1

comm-mode = angular

nstcomm = 100

bd-fric = 0

ld-seed = -1

nstxout = 1000

nstvout = 500000

nstfout = 500000

nstlog = 100

nstcalcenergy = 100

nstenergy = 1000

nstxtcout = 100

xtc-precision = 1000

xtc-grps = system

energygrps = system

cutoff-scheme = group

nstlist = 1

ns-type = simple

pbc = no

rlist  = 0.5

coulombtype= cut-off

rcoulomb = 0.5

vdw-type = Cut-off

vdw-modifier = Potential-shift-Verlet

rvdw-switch = 0.8

rvdw= 0.5

table-extension = 1

fourierspacing = 0.12

fourier-nx= 0

fourier-ny = 0

fourier-nz = 0

implicit-solvent = GBSA

gb-algorithm = still

nstgbradii = 1

rgbradii = 0.5

gb-epsilon-solvent = 80

sa-algorithm = Ace-approximation

sa-surface-tension = 2.05

tcoupl  = Nose-Hoover

tc-grps = system

tau-t  = 0.1

ref-t = 298.00

pcoupl = parrinello-rahman

pcoupltype = Isotropic

tau-p   = 1.0

compressibility   = 4.5e-5

ref-p   = 1.0

refcoord-scaling = No

gen-vel   = no

gen-temp = 298.00

gen-seed   = -1

constraints  = all-bonds

constraint-algorithm   = Lincs

continuation  = yes

Shake-SOR  = no

shake-tol  = 0.0001

lincs-order = 4

lincs-iter   = 1

lincs-warnangle  = 30


*mdp file for MD*

integrator  = md

tinit = 0

dt  = 0.001

nsteps = 500000000 ; 1 us

init-step = 0

simulation-part= 1

comm-mode  = Angular

nstcomm = 100

comm-grps = system

bd-fric  = 0

ld-seed = -1

nstxout  = 10000

nstvout  = 0

nstfout   = 0

nstlog  = 10000

nstcalcenergy = 10000

nstenergy = 10000

nstxtcout  = 0

xtc-precision  = 1000

xtc-grps  = system

energygrps  = system

cutoff-scheme  = group

nstlist  = 10

ns-type  = simple

pbc   = no

rlist    = 0.5

coulombtype    = cut-off

rcoulomb  = 0.5

vdw-type  = Cut-off

vdw-modifier  = Potential-shift-Verlet

rvdw-switch = 0.8

rvdw  = 0.5

DispCorr = No

table-extension  = 500

fourierspacing = 0.12

fourier-nx  = 0

fourier-ny = 0

fourier-nz = 0

implicit-solvent = GBSA

;implicit-solvent = GBSA

gb-algorithm = still

nstgbradii = 1

rgbradii = 0.5

gb-epsilon-solvent = 80

sa-algorithm = Ace-approximation

sa-surface-tension = 2.05

tcoupl = v-rescale

nsttcouple = -1

nh-chain-length = 10

print-nose-hoover-chain-variables = no

tc-grps = system

tau-t  = 0.1

ref-t = 298.00

pcoupl = No

pcoupltype = Isotropic

nstpcouple = -1

tau-p  = 1

refcoord-scaling = No

gen-vel = no

gen-temp = 298.00

gen-seed  = -1

constraints  = none

constraint-algorithm = Lincs

continuation = yes

Shake-SOR = no

shake-tol = 0.0001

lincs-order = 4

lincs-iter = 1

lincs-warnangle = 30

morse = no

free-energy = yes

couple-lambda0 = vdw-q

couple-lambda1= vdw-q

couple-intramol = no

init-lambda = 0

delta-lambda = 0.1

nstdhdl  = 50

calc-lambda-neighbors  = 1

dhdl-print-energy = no

sc-alpha = 0

sc-power= 1

sc-r-power  = 6

sc-sigma= 0.3

sc-coul = no

separate-dhdl-file = yes

dhdl-derivatives  = yes

dh_hist_size  = 0

dh_hist_spacing = 0.1