[gmx-users] REMD implicit solvent

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Fri Jan 5 13:22:06 CET 2018


Hi,

I should run it by using mdrun_mpi?

best
Urszula

> Hello,
>
>  From my experience, the domain decomposition is not compatible with
> implicit solvent, you have to switch
> to particle decomposition for the simulations.
>
>
> All the best,
> Qinghua
>
> On 01/05/2018 12:40 PM, Urszula Uciechowska wrote:
>> 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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--------------------------------------------
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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