[gmx-users] Multiple LINCS Warnings in NVT Equillibration

[Matthew Zwier]

Try using -DFLEXIBLE in your minimization prior to running NVT.

MZ


On Tue, Jul 9, 2013 at 10:22 AM, ashish24294 <ashish24294 at yahoo.co.in>wrote:

> I am simulating one urea molecule in water and am struggling with it
> nvt.log
> <http://gromacs.5086.x6.nabble.com/file/n5009701/nvt.log>
>
>
>
> *The .mdp for energy minimization is*
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 100.0         ; Stop minimization when the maximum force
> < 1000.0
> kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps
> to perform
> energygrps      = URE
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1             ; Frequency to update the neighbor list
> and long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> coulombtype     = PME           ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0           ; Short-range electrostatic cut-off
> rvdw            = 1.0           ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>
>
>
>
> /*And the nvt.mdp is:
> */
> title       = UREA_in_WATER NVT equillibration
>
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 50000     ; 2 * 50000 = 100 ps
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 100       ; save coordinates every 0.2 ps
> nstvout     = 100       ; save velocities every 0.2 ps
> nstenergy   = 100       ; save energies every 0.2 ps
> nstlog      = 100       ; update log file every 0.2 ps
> energygrps  = URE
> ; Bond parameters
> continuation    = no            ; 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
> ns_type     = grid      ; search neighboring grid cells
> nstlist     = 5         ; 10 fs
> rlist       = 0.75       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.75       ; short-range electrostatic cutoff (in nm)
> rvdw        = 0.75       ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = URE_Water    ; two coupling groups - more accurate
> tau_t       = 0.1                                     ; time constant, in
> ps
> ref_t       = 300                       ; reference temperature, one for
> each group, in K
> ; Pressure coupling
> 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
>
> *The resultant nvt.log has been attached*
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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