[gmx-users] REMD implicit solvent

[Mark Abraham]

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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