[gmx-users] conjugate gradient with dummies

[DimitryASuplatov]

Hello,
I am trying to run two step energy minimization with steep followed by
cg on a structure with hydrogen vsites and heavyh (in OPLSAA). In
gromacs 3.3.3 I had an error in grompp when starting cg - it reported
that cg was incompatible with constraint bonds (LINCS was off, I guess
it was about dummy sites). Not in 4.0.2 I receive an error from mdrun -
system explodes complaining about deviation in bond length after LINCS,
though it is off.

Two questions:
1/ Can I use cg with dummies?
2/ It there any (scientific) advantage of using steep+cg except for
speed?

Thanks

Steep and CG mdp files are below

=======================================================================
;-------------PREPROCESSING OPTIONS------------
title                       = "Energy minimization"
cpp                         =  /usr/bin/cpp; my C prepocessor
(whereIsIt)
include                     = ; dir to include in my topology file
define                      = ;

;-------------RUN CONTROL---------------------
integrator        = steep;

;-------------START TIME & TIMESTEP-----------
nsteps              =  5000 ; (0) maximum number of steps to integrate
nstcomm             =  1

;-------------NEIGHBOR SEACHING---------------
nstlist                                       = 5; frequency o update
neighbor list
ns_type                                       = grid; make a gid in the
box and check only
;neighboring grid cell when constructing a new neighbor list
rlist                                         = 1.0; cut-off distance
for the short-range neighbor list

;-------------ELECTROSTATICS------------------
coulombtype              = Reaction-field  ; reaction field with coulomb
cut-off rcoulomb
rcoulomb                                      = 1.5 ;distance for the
coulomb cut-off
epsilon_rf                                     = 80;dielectric constant
epsilon_r                                       = 1;
vdwtype                                       = cut-off; twin-range
cut-off`s with neighbor list cut-off rlist
;and VdW cut-off rvdw, where rvdw>rlist
rvdw                                          = 1.0 ; distance for for
the LJ or Buckingam cut-off

;-------------ENERGY MINIMIZATION-------------
emtol                = 500 (kJ/mol*nm); minimisation is converged when
the maximum force is smaller then this value
emstep               = 0.01; initial step size

;-------------TEMTERAURE CONTROL--------------
tcoupl                   = v-rescale
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 0
ld_seed                  = 24564314

;--------- PRESSURE CONTROL---------------------
Pcoupl                   = no
Pcoupltype               = Isotropic
tau-p                    = 1
ref_p                    = 1
compressibility          = 4.5E-5

;------------ VELOCITY INITIATION -----------------------
gen-vel                  = no
gen-temp                 = 0

;------------- BONDS -----------------------
constraints              = none
constraint-algorithm     = Lincs
unconstrained-start      = yes
Shake-SOR                = no
shake-tol                = 0.0001
lincs-order              = 8
lincs-warnangle          = 30
lincs-iter               = 8

============================================================================


;-------------PREPROCESSING OPTIONS------------
title                       = "Energy minimization"
cpp                         =  /usr/bin/cpp; my C prepocessor
(whereIsIt)

;-------------RUN CONTROL---------------------
integrator        = cg;

;-------------START TIME & TIMESTEP-----------
nsteps              =  5000 ; (0) maximum number of steps to integrate
nstcomm             =  1

;-------------NEIGHBOR SEACHING---------------
nstlist                                       = 5; frequency o update
neighbor list
ns_type                                       = grid; make a gid in the
box and check only
;neighboring grid cell when constructing a new neighbor list
rlist                                         = 1.0; cut-off distance
for the short-range neighbor list

;-------------ELECTROSTATICS------------------
coulombtype                                     = Reaction-field  ;
reaction field with coulomb cut-off rcoulomb
rcoulomb                                        = 1.5 ;distance for the
coulomb cut-off
epsilon_rf                                      = 80;dielectric constant
epsilon_r                                       = 1;
vdwtype                                         = cut-off; twin-range
cut-off`s with neighbor list cut-off rlist
;and VdW cut-off rvdw, where rvdw>rlist
rvdw                                            = 1.0 ; distance for for
the LJ or Buckingam cut-off

;-------------ENERGY MINIMIZATION-------------
emtol                = 100 (kJ/mol*nm); minimisation is converged when
the maximum force is smaller then this value
emstep               = 0.01; initial step size
nstcgsteep           = 1000

;-------------TEMTERAURE CONTROL--------------
tcoupl                   = v-rescale
tc-grps                  = System
tau-t                    = 0.1
ref-t                    = 0
ld_seed                  = 24564314

;--------- PRESSURE CONTROL---------------------
Pcoupl                   = no
Pcoupltype               = Isotropic
tau-p                    = 1
ref_p                    = 1
compressibility          = 4.5E-5

;------------ VELOCITY INITIATION -----------------------
gen-vel                  = no
gen-temp                 = 0

;------------- BONDS -----------------------
constraints              = none
constraint-algorithm     = Lincs
unconstrained-start      = yes
Shake-SOR                = no
shake-tol                = 0.0001
lincs-order              = 8
lincs-warnangle          = 30
lincs-iter               = 8
morse                    = yes