[gmx-users] REMD implicit solvent

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Fri Jan 5 12:46:45 CET 2018


Hi,

I just run a normal single-replica. Now the error that I have is:

Program mdrun_mpi, VERSION 4.5.5
Source code file: domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Any suggestions? What can I do to run it?

Thanks
Ula

> Hi,
>
> Did you try to debug your setup by running a normal single-replica
> simulation first?
>
> Mark
>
> On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska <
> urszula.uciechowska at biotech.ug.edu.pl> wrote:
>
>>
>>
>> Dear gromacs users,
>>
>> I am trying to run REMD simulations using 4.5.5 version (implicit
>> solvent). The MD procedure:
>>
>> pdb2gmx -f  prot.pdb -o prot.gro -q prot.pdb -ignh -ss.
>>
>> The input for minimization step:
>>
>> ; Run control parameters
>> integrator           = cg
>> nsteps               = 8000000
>> vdwtype              = cut-off
>> coulombtype          = cut-off
>> ;cutoff-scheme        = group
>> pbc                  = no
>> periodic_molecules   = no
>> nstlist              = 10
>> ns_type              = grid
>> rlist                = 1.0
>> rcoulomb             = 1.6
>> rvdw                 = 1.6
>> comm-mode            = Angular
>> nstcomm              = 10
>> ;
>> ;Energy minimizing stuff
>> ;
>> emtol                = 100.0
>> nstcgsteep           = 2
>> emstep               = 0.01
>> ;
>> ;Relative dielectric constant for the medium and the reaction field
>> epsilon_r                = 1
>> epsilon_rf               = 1
>> ;
>> ; Implicit solvent
>> ;
>> implicit_solvent     = GBSA
>> gb_algorithm         = OBC          ;Still  HCT   OBC
>> nstgbradii           = 1.0
>> rgbradii             = 1.0          ; [nm] Cut-off for the calculation
>> of
>> the Born radii. Currently must be equal to rlist
>> gb_epsilon_solvent   = 80           ; Dielectric constant for the
>> implicit
>> solvent
>> gb_saltconc          = 0            ; Salt concentration for implicit
>> solvent models, currently not used
>> sa_algorithm         = Ace-approximation
>> sa_surface_tension   = 2.05016      ; Surface tension (kJ/mol/nm^2) for
>> the SA (nonpolar surface) part of GBSA. The value -1 will set default
>> value for Still/HCT/OBC GB-models.
>>
>> and it finished without errors.
>>
>> The problem is with equilibration step. The input file that I used is:
>>
>> ; MD CONTROL OPTIONS
>> integrator              = md
>> dt                      = 0.002
>> nsteps                  = 50000         ; 10 ns
>> init_step               = 0            ; For exact run continuation or
>> redoing part of a run
>> comm-mode               = Angular      ; mode for center of mass motion
>> removal
>> nstcomm                 = 10           ; number of steps for center of
>> mass motion removal
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout                  = 1000
>> nstvout                  = 1000
>> nstfout                  = 1000
>>
>> ; Output frequency for energies to log file and energy file
>> nstlog                   = 1000
>> nstcalcenergy            = 10
>> nstenergy                = 1000
>>
>> ; Neighbor searching and Electrostatitcs
>> vdwtype              = cut-off
>> coulombtype          = cut-off
>> ;cutoff-scheme        = group
>> pbc                  = no
>> periodic_molecules   = no
>> nstlist              = 5
>> ns_type              = grid
>> rlist                = 1.0
>> rcoulomb             = 1.6
>> rvdw                 = 1.0
>> ; Selection of energy groups
>> energygrps               = fixed not_fixed
>> freezegrps               = fixed not_fixed
>> freezedim                = Y Y Y N N N
>>
>> ;Relative dielectric constant for the medium and the reaction field
>> epsilon_r                = 1
>> epsilon_rf               = 1
>>
>> ; Temperutare coupling
>> tcoupl                   = v-rescale
>> tc_grps                  = fixed not_fixed
>> tau_t                    = 0.01 0.01
>> ;nst_couple               = 5
>> ref_t                    = 300.00 300.00
>>
>> ; Pressure coupling
>> pcoupl                   = no
>> ;pcoupletype              = isotropic
>> tau_p                    = 1.0
>> ;compressiblity           = 4.5e-5
>> ref_p                    = 1.0
>> gen_vel                  = yes
>> gen_temp                 = 300.00 300.00
>> gen_seed                 = -1
>> constraints              = h-bonds
>>
>>
>> ; Implicit solvent
>> implicit_solvent         = GBSA
>> gb_algorithm             = Still ; HCT  ; OBC
>> nstgbradii               = 1.0
>> rgbradii                 = 1.0          ; [nm] Cut-off for the
>> calculation
>> of the Born radii. Currently must be equal to rlist
>> gb_epsilon_solvent       = 80           ; Dielectric constant for the
>> implicit solvent
>> gb_saltconc              = 0            ; Salt concentration for
>> implicit
>> solvent models, currently not used
>> sa_algorithm             = Ace-approximation
>> sa_surface_tension       = 2.05016      ; Surface tension (kJ/mol/nm^2)
>> for the SA (nonpolar surface) part of GBSA. The value -1 will set
>> default
>> value for Still/HCT/OBC GB-models.
>>
>>
>> mdrun -v -multidir eq_[12345678]
>>
>> The error that I obtained is:
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> I do not know what is wrong. I checked the Fatal error at
>> www.gromacs.org/Documentation/Errors. My system is ok, I tried to
>> increase
>> the min steps but did not help. I have also checked the
>> http://www.gromacs.org/Documentation/How-tos/REMD but can not move
>> forward
>> because of equilibration step.
>>
>> I appreciate any recommendation.
>>
>> Thanks
>>
>> Urszula
>>
>>
>> --------------------------------------------
>> Urszula Uciechowska PhD
>> University of Gdansk and Medical Univesity of Gdansk
>> Department of Molecular and Cellular Biology
>> ul. Abrahama 58
>> 80-307 Gdańsk
>> Poland
>>
>>
>> -----------------------------------------
>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> http://www.ug.edu.pl/
>>
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--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland


-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/



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