[gmx-users] REMD implicit solvent

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Fri Jan 5 12:11:44 CET 2018



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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