[gmx-users] LINCS warning

[Mark Abraham]

Hi,

That tends to suggest either your ligand conformation or ligand parameters
are not appropriate. What happens with ligand in vacuo with EM and then NVE
with a very small time step, e.g. 0.00005 ps?

Mark

On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli <faryal.tavakoli at gmail.com>
wrote:

> 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
> --
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