[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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