[gmx-users] REMD implicit solvent
Qinghua Liao
scorpio.liao at gmail.com
Fri Jan 5 12:56:07 CET 2018
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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