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

[Justin Lemkul]

On 10/24/14 8:31 AM, Nizar Masbukhin wrote:
> 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
>

You need to simplify significantly to determine what the issue is.  You're using 
(1) very short cutoffs, (2) free energy, and (3) implicit solvent.  Any 
combination of those might be causing the problem you're having.  Generally, 
extra long cutoffs are used in implicit environments.  Try a "normal" run 
without the free energy code going and see if that improves the situation.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================