[gmx-users] Lincs warning_set GMX_MAXCONSTRWARN to -1

[Anjali Patel]

Hello users,

Yes i have gone through all lincs warning from the errors and also i have
refer user mailing list for this trouble. But i am not getting the answer.
i am doing MD simulation in which i have minimized system number of times
and my "em.mdp" file is blowed.

; LINES STARTING WITH ';' ARE COMMENTS
title               = Minimization      ; Title of run

; 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
< 10.0 kJ/mol
emstep          = 0.002      ; Energy step size
nsteps              = 50000             ; Maximum number of (minimization)
steps to perform
nbfgscorr         = 10
constraints       = none
; Parameters describing how to find the neighbors of each atom and how to
calculate the intee
ractions
nstlist             = 1                 ; Frequency to update the neighbor
list and long rann
ge forces
cutoff-scheme   = Verlet
ewald_rtol      = 1e-6
ns_type             = grid                  ; Method to determine neighbor
list (simple, grii
d)
rlist               = 1.2                   ; Cut-off for making neighbor
list (short range
forces)
coulombtype         = PME                   ; Treatment of long range
electrostatic interactt
ions
rcoulomb            = 1.2                   ; long range electrostatic
cut-off
vdwtype         = cutoff

1,1           Top

em.log file is

Steepest Descents converged to machine precision in 400 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -6.1178244e+05
Maximum force     =  7.0838816e+07 on atom 14616
Norm of force     =  6.4604380e+05

after that i have gone through this and in some cases it can be possible
that convergence can not reach the requested force.

now i am doing NVT and my NVT.msp is belowed
title                   = Protein-ligand complex NVT equilibration
define                  = -DFLEXIBLE  ; position restrain the protein and
ligand
; Run parameters
integrator              = md        ; leap-frog integrator
dt                      = 0.002     ; 2 fs
nsteps                  = -1     ; 2 * 5000 = 10 ps
; Output control
nstenergy               = 10   ; save energies every 1.0 ps
nstlog                  = 10   ; update log file every 1.0 ps
nstxout-compressed      = 1   ; save coordinates every 1.0 ps
energygrps              = UNK_JDN Water
; Bond parameters
continuation            = no        ; first dynamics run
constraints             = all-bonds   ; bonds to H are constrained
constraint-algorithm    = lincs
;shake-tol               = 0.0001
lincs_order             = 8         ; also related to accuracy
lincs-iter              = 2         ; accuracy of LINCS
lincs-warnangle         = 10
; Neighbor searching and vdW
cutoff-scheme           = Verlet
coulombtype             = PME
rcoloumb                = 1.0
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 20        ; largely irrelevant with Verlet
coulomb-modifier        = Potential-shift-Verlet
;nstcomm                 = 100
rlist                   = 0.9
vdwtype                 = PME
vdw-modifier            = Potential-shift-Verlet
;rvdw-switch             = 1.0
rvdw                    = 1.0       ; short-range van der Waals cutoff (in
nm)
DispCorr                = EnerPres
; Electrostatics
;coulombtype             = PME       ; Particle Mesh Ewald for long-range
electrostatics
;rcoulomb                = 1.4       ; short-range electrostatic cutoff (in
nm)
pme_order               = 8         ; cubic interpolation
fourierspacing          = 0.16      ; grid spacing for FFT
ewald-rtol              = 2.5e-5
; Temperature coupling
tcoupl                  = V-rescale                     ; modified
Berendsen thermostat
tc-grps                 = UNK_JDN Water      ; two coupling groups - more
accurate
tau_t                   = 0.1  0.1                      ; time constant, in
ps
ref_t                   = 300  300
nsttcouple             =  10                     ; reference temperature,
one for each group, in K
; Pressure coupling
pcoupl                  = Berendsen        ; no pressure coupling in NVT
periodic_molecules      = no
nstpcouple              =  20
pcoupltype              = isotropic
tau-p                   =  3
compressibility         = 4.5e-5
ref-p                   = 1.0
refcoord-scaling        = all
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
;DispCorr                = no
; Velocity generation
gen_vel                 = no       ; assign velocities from Maxwell
distribution
gen_temp                = 300       ; temperature for Maxwell distribution
gen_seed                = -1        ; generate a random seed


and i am getting this error

Fatal error:
Too many LINCS warnings (16238)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

how can i resolve this error?
also in my .log file showing this kind of error

Warning: pressure scaling more than 1%, mu: 153.128 153.128 153.128
   Energies (kJ/mol)

how can i control the pressure?
thank you in advance.

With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002