[gmx-users] error in the middle of running mdrun_mpi
Nizar Masbukhin
nizar.fkub08 at gmail.com
Sun Oct 26 14:55:21 CET 2014
regarding gaining speed in implicit solvent simulation, i have tried to
parallelize using -ntmpi flag. However gromacs doesn't allow as i use group
cutoff-scheme. Any recommendation how to parallelise implicit solvent
simulation? I do need parallelise my simulation. I have found the same
question in this mail list, one suggest use all-vs-all kernel which uses
zero cut-off.
This is my test run actually. I intend to run my simulation in cluster
computer.
On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/26/14 9:17 AM, Nizar Masbukhin wrote:
>
>> Thanks Justin.
>> I have increased the cutoff, and yeah thats work. There were no error
>> message anymore. The first 6 nanoseconds, i felt the simulation run
>> slower.
>> Felt so curious that simulation run very fast the rest of time.
>>
>>
> Longer cutoffs mean there are more interactions to calculate, but the
> cutoffs aren't to be toyed with arbitrarily to gain speed. They are a
> critical element of the force field itself, though in implicit solvent, it
> is common to increase (and never decrease) the cutoff values used in
> explicit solvent. Physical validity should trump speed any day.
>
> -Justin
>
>
> On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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--
Thanks
My Best Regards, Nizar
Medical Faculty of Brawijaya University
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