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

[Nizar Masbukhin]

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.

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
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Thanks
My Best Regards, Nizar
Medical Faculty of Brawijaya University