[gmx-users] too many lincs warnings

[Meenakshi Rajput]

Thanks..
On Aug 20, 2014 1:29 PM, "Meenakshi Rajput" <ashi.rajput39 at gmail.com> wrote:

> hello users
> I had done energy minimisation of protein-ligand complex and i got
> negative potential. Also the ligand was at right place after EM run but
> when I tried the positional restrained run, too many lincs warnings came
> and md run stopped suddenly. I am using charmm force field and mdp file
> settings for position restrined run are:-
> define        = -DPOSRES    ; position restrain the protein
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 50000        ; 2 * 50000 = 100 ps
> dt        = 0.002        ; 2 fs
> ; Output control
> nstxout        = 500        ; save coordinates every 0.2 ps
> nstvout        = 500        ; save velocities every 0.2 ps
> nstenergy    = 500        ; save energies every 0.2 ps
> nstlog        = 500        ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes        ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter    = 1        ; accuracy of LINCS
> lincs_order    = 4        ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type        = grid        ; search neighboring grid cells
> nstlist        = 10        ; 10 fs
> rlist        = 1.2        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.2        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.2        ; short-range van der Waals cutoff (in nm)
> rvdw-switch     = 1.0
> ; Electrostatics
> coulombtype    = PME        ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order    = 4        ; cubic interpolation
> fourierspacing    = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more
> accurate
> tau_t        = 0.1    0.1    ; time constant, in ps
> ref_t        = 300     300    ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl        = no         ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc        = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = yes        ; assign velocities from Maxwell distribution
> gen_temp    = 300        ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Please tell me if there is something wrong with mdp settings or is it some
> other problem?
>
>