[gmx-users] Gromacs multisubunit defragmentation

[Muhammad Hagras]

Hi folks,

I need some help in running EM on three subunits protein (not covalently
bonded),

When I run EM on such molecule in vacuum or in implicit solvent, the three
subunits move apart ?! I tried with and without pbc and with and without
implicit solvent and still the same results!


Here is my minim.mdp I used
-------------------------------------------------------------------
title           = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp             = /lib/cpp      ; Preprocessor

; Define can be used to control processes
define          = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator      = cg            ; Algorithm (steep = steepest descent
minimization)
emtol           = 10.0          ; Stop minimization when the maximum force
< 1.0 kJ/mol
nstcalclr       = 1
nstcgsteep      = 10000
dt              = 0.001
nsteps          = 1000000000            ; Maximum number of (minimization)
steps to perform
nstenergy       = 10000         ; Write energies to disk every nstenergy
steps
energygrps      = System        ; Which energy group(s) to write to disk
;freezegrps     = Backbone
;freezedim      = Y Y Y
rlist           = 1.0
lincs_order     = 8
lincs_iter      = 4
nstcomm         = 1
nstcalcenergy   = 1
cutoff-scheme = group

comm_mode       = Linear
;nstcomm        = 1
;dispcorr       = EnerPres
;optimize_fft   = yes
;pme_order      = 6
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type         = grid;simple   ; Method to determine neighbor list
(simple, grid)
coulombtype     = PME;cut-off   ; Treatment of long range electrostatic
interactions
vdwtype         = cut-off
rcoulomb        = 1.0           ; long range electrostatic cut-off
rvdw            = 1.0   ; long range Van der Waals cut-off
;constraints    = all-bonds             ; Bond types to replace by
constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)i


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = no;gbsa

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still;OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 1.0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 4
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
gb_dielectric_offset     = 0.009
sa_algorithm             = Ace-approximation
; 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.
sa_surface_tension       = 2.25936

-----------------------------------------------------------------------

Thanks for help,

Muhammad Hagras
PhD, Biophysics UCD