[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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