[gmx-users] LINCS WARNING relative constraint deviation

[E. Nihal Korkmaz]

Dear all,

I am trying to simulate a GB simulation of a 112 amino acid long protein. I
keep getting these errors,

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 27718, time 55.436 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.058237, max 1.390675 (between atoms 91 and 93)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     91     92   50.2    0.1016   0.1065      0.1010
     91     93   90.0    0.1002   0.2415      0.1010
     91     94   70.2    0.1025   0.1066      0.1010
     79     80   90.0    0.1057   1.0667      0.1090
     79     81   90.0    1.3066  47.9342      0.1090
     85     86   90.0    0.1084   0.1758      0.1090
     85     87   90.0    1.0654   0.1668      0.1090
     88     89   90.0    0.1097   0.6994      0.1090
     88     90   90.0    0.1125   0.1097      0.1090
     91     92   50.2    0.1016   0.1065      0.1010
     91     93   90.0    0.1002   0.2415      0.1010
     91     94   70.2    0.1025   0.1066      0.1010


I am copying my mdp parameters below, I'd appreciate any suggestions to fix
that.

integrator               = sd
tinit                    = 0
dt                       = 0.002
nsteps                   = 2500000
simulation_part          = 1
init_step                = 1

nstxout                  = 5000
nstvout                  = 5000
nstenergy                = 500
nstxtcout                = 500
nstlog                   = 500

xtc_grps                 = System
energygrps               = System
comm_mode                = Linear
; neighbor searching and vdw/pme setting up
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 2.0

implicit_solvent         = GBSA
gb_algorithm             = OBC
gb_saltconc              = 0.15
rgbradii                 = 2.0

coulombtype              = Cut-off
fourierspacing           = 0.1
pme_order                = 6
rcoulomb                 = 2.0

vdwtype                  = Cut-off
rvdw_switch              = 1.0
rvdw                     = 2.0

; cpt control
tcoupl                   = V-rescale
tc-grps                  = System
tau_t                    = 0.1
ref_t                    = 300.0

Pcoupl                   = Berendsen
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; velocity & temperature control
gen_vel                  = yes
gen_temp                 = 300.0
annealing                = no
constraints              = hbonds
constraint_algorithm     = lincs
morse                    = no


Thanks,
-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   korkmaz at wisc.edu
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