[gmx-users] LINCS error

[aiswarya pawar]

Hi users,

I did energy minimization of a protein complex using the following
minimization mdp file.

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

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          = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1.0 kJ/mol
emstep      = 0.01
nsteps = 5000 ; Maximum number of (minimization) steps to perform
nstenergy = 10 ; Write energies to disk every nstenergy steps
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
ns_type = grid   ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.4 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc    = xyz ; Periodic Boundary Conditions (yes/no)


and the pr.mdp =

; VARIOUS PREPROCESSING OPTIONS
title                    = Position Restrained Molecular Dynamics
define                   = -DPOSRES

constraints              = all-bonds
integrator               = md
dt                       = 0.001 ; ps !
nsteps                   = 25000 ; total 50 ps.
nstcomm                  = 10
nstxout                  = 500 ; collect data every 1 ps
nstxtcout                = 500
nstvout                  = 0
nstfout                  = 0
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.0
vdwtype                  = cut-off
rvdw                     = 1.4
pme_order                = 4
ewald_rtol               = 1e-5
optimize_fft             = yes
DispCorr                 = no
; Berendsen temperature coupling is on
Tcoupl                   = v-rescale
tau_t                    = 0.1 0.1
tc-grps = protein non-protein
ref_t                    = 300 300
; Pressure coupling is on
Pcoupl                   = parrinello-rahman
Pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
; Generate velocites is on at 300 K.
gen_vel                  = yes
gen_temp                 = 300.0
gen_seed                 = -1

and md.mdp file =

; VARIOUS PREPROCESSING OPTIONS
title                    = Position Restrained Molecular Dynamics


; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 2500000 ; total 5000 ps.
nstcomm = 10
nstxout = 500 ; collect data every 1 ps
nstxtcout = 0
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = -1


The minimization step went well. but while doing the final mdrun am getting
LINCS error. i read through the numerous mailing list on grimaces but still
couldn't understand how would i fix this. am getting this error for all the
10 protein complex i did minimization for. Please help.


Thanks,
Aiswarya
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