[gmx-users] LINCS warning

[Farial Tavakoli]

Dear gromacs users

I am trying to simulate a complex, including a protein and a peptidec
ligand with 2 phosphotyrosine residues.
The protein topology was generated using amber99sb.ff in gromacs and the
ligand topology was generated using ff99sb in amber tools 16, then the
.inpcrd and .prmtop files were converted to .gmx and .top files using
acpype python script.
*python acpype.py -p prmtop -x inpcrd*
.itp file was created by removing  header and footer of .top file.
Then .gro and .top files were modified according to the tutorial in
gromacs.
I tryed to minimize the complex , but it stoped before 100 steps :





*Steepest Descents converged to machine precision in 80 steps,but did not
reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
force     =  7.0647156e+04 on atom 5256Norm of force     =  5.8775842e+02*

and when I run NVT simulation , faced to LINCS warning:










*starting mdrun 'Protein in water'200000 steps,    400.0 ps.step 0Step 5,
time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
length   5258   5261   90.0    0.0960   0.1665      0.0960   5283   5286
90.0    0.0960   0.1425      0.0960Wrote pdb files with previous and
current coordinates*
I separated my complex in to protein and ligand and simulated the protein
alone in the TIP3P water model. that was stable. then, simulated the ligand
in vacuo and faced with LINCS warning.
Both force fields that were used to generate topologies were AMBER99sb, Is
it possible its because of .mdp files which I used?
Would you please reply and advice me how I can resolve this problem?

best regards
Farial

the em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep
emtol       = 1000.0
emstep      = 0.01
nsteps      = 50000
nstlist         = 1
cutoff-scheme   = Verlet
ns_type         = grid
coulombtype     = PME
rcoulomb        = 1.0
rvdw            = 1.0
pbc             = xyz

nvt.mdp file:
title                   = AMBER  NVT equilibration
define                  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator              = md
nsteps                  = 200000     ; 2 * 200000 = 400 ps
dt                      = 0.002
; Output control
nstxout                 = 500
nstvout                 = 500
nstenergy               = 500
nstlog                  = 500
; Bond parameters
continuation            = no
constraint_algorithm    = lincs
constraints             = h-bonds
lincs_iter              = 1
lincs_order             = 4
; Nonbonded settings
cutoff-scheme           = Verlet
ns_type                 = grid
nstlist                 = 10
rcoulomb                = 1.0
rvdw                    = 1.0
; Electrostatics
coulombtype             = PME
pme_order               = 4
fourierspacing          = 0.16
; Temperature coupling is on
tcoupl                  = V-rescale
tc-grps                 = Protein Non-Protein
tau_t                   = 0.1     0.1
ref_t                   = 300     300
; Pressure coupling is off
pcoupl                  = no
; Periodic boundary conditions
pbc                     = xyz
; Velocity generation
gen_vel                 = yes
gen_temp                = 300
gen_seed                = -1