[gmx-users] Multiple LINCS Warnings in NVT Equillibration

[Justin Lemkul]

On 7/9/13 10:22 AM, ashish24294 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)

These cutoffs don't make sense for any of the force fields within Gromacs.  This 
is the most likely source of instability outside the topology itself.

-Justin

> ; 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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