[gmx-users] rotation of atoms by more than 90 degrees & LINCS Warnings

[Dan Gil]

Hi Sagar,

At which time step do you get LINCS warnings?

Also, please see:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Dan

On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbathla4 at gmail.com> wrote:

> Dear all,
>
> My system consists of 2 orthorhombic parallel graphene sheets in a big
> triclinic box filled with water. when i am trying to run equillibration
> then i am getting too many lincs warnings and simulation has been getting
> crashed everytime. i have put retraint on all atoms of graphene but still
> this problem is occuring again.
>
> My .mdp file looks like this
> title           = OPLS Graphene IN WATER NVT equilibration
> define          = -DPOSRES -DFLEXIBLE   ; position restrain the protein
>
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 500000                ; 2 * 500000 = 1000 ps
>
> dt                  = 0.002             ; 2 fs
>
> ; Output control
> nstxout         = 1000          ; save coordinates every 1.0 ps
> nstvout         = 1000          ; save velocities every 1.0 ps
> nstenergy       = 1000          ; save energies every 1.0 ps
> nstlog          = 1000          ; update log file every 1.0 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
> lincs-warnangle             = 90
>
> ; Neighborsearching
> vdw-modifier            = Force-switch
> cutoff-scheme   = Verlet
> ns_type             = grid              ; search neighboring grid cells
> nstlist             = 10                ; 20 fs, largely irrelevant with
> Verlet
> rcoulomb            = 1.2               ; short-range electrostatic cutoff
> (in nm)
> rvdw                = 1.2
> rlist               = 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          = nose-hoover               ; nose-hoover thermostat
> tc-grps         = GRA SOL       ; 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
> periodic-molecules = yes
>
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
>
> ; number of steps for center of mass motion removal =
> comm-mode                = Linear
> nstcomm                  = 1
> comm-grps                = GRA SOL
> ; Velocity generation
> gen_vel         = no            ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
> ;non equillibrium md
> freezegrps: GRA
> freezedim: Y Y Y
>  i have tried various things but nothing is working.
> please help to solve this problem
>
> Regards
> Sagar Bathla
> --
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