[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

[Justin Lemkul]

On 2/9/15 7:34 AM, Antara mazumdar wrote:
> ​eRROR OBTAINED DURING NVT:
>
> ​
> Water molecule starting at atom 673675 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> ​NVT CONDITIONS WERE :
> ​
>
> n for B2AR-POPC system
> define          = -DPOSRES      ; Protein is position restrained (uses the
> posres.itp file information)
> ; Parameters describing the details of the NVT simulation protocol
> integrator      = md            ; Algorithm ("md" = molecular dynamics
> [leap-frog integrator]; "md-vv" = md using velocity verlet; sd = stochastic
> dynamics)
> dt              = 0.002         ; Time-step (ps)
> nsteps          = 250000        ; Number of steps to run (0.002 * 250000 =
> 500 ps)
>
> ; Parameters controlling output writing
> nstxout         = 1000          ; Write coordinates to output .trr file
> every 2 ps
> nstvout         = 1000          ; Write velocities to output .trr file
> every 2 ps
> nstenergy       = 1000          ; Write energies to output .edr file every
> 2 ps
> nstlog          = 1000          ; Write output to .log file every 2 ps
>
> ; Parameters describing neighbors searching and details about interaction
> calculations
> ns_type         = grid          ; Neighbor list search method (simple, grid)
> nstlist         = 5             ; Neighbor list update frequency (after
> every given number of steps)
> rlist           = 1.2           ; Neighbor list search cut-off distance (nm)
> rcoulomb        = 1.2           ; Short-range Coulombic interactions
> cut-off distance (nm)
> rvdw            = 1.2           ; Short-range van der Waals cutoff distance
> (nm)
> pbc             = xyz           ; Direction in which to use Perodic
> Boundary Conditions (xyz, xy, no)
>
> ; Parameters for treating bonded interactions
> continuation    = no            ; Whether a fresh start or a continuation
> from a previous run (yes/no)
> constraint_algorithm = LINCS    ; Constraint algorithm (LINCS / SHAKE)
> constraints     = all-bonds     ; Which bonds/angles to constrain
> (all-bonds / hbonds / none / all-angles / h-angles)
> lincs_iter      = 2             ; Number of iterations to correct for
> rotational lengthening in LINCS (related to accuracy)
> lincs_order     = 8             ; Highest order in the expansion of the
> constraint coupling matrix (related to accuracy)
>
> ; Parameters for treating electrostatic interactions
> coulombtype     = PME           ; Long range electrostatic interactions
> treatment (cut-off, Ewald, PME)
> pme_order       = 4             ; Interpolation order for PME (cubic
> interpolation is represented by 4)
> fourierspacing  = 0.16          ; Maximum grid spacing for FFT grid using
> PME (nm)
>
> ; Temperature coupling parameters
> tcoupl          = V-rescale             ; Modified Berendsen thermostat
> using velocity rescaling
> tc-grps         = Protein DOPC SOL_NA   ; Define groups to be coupled
> separately to temperature bath
> tau_t           = 0.1   0.1     0.1     ; Group-wise coupling time constant
> (ps)
> ref_t           = 300   300     300     ; Group-wise reference temperature
> (K)
>
> ; Pressure coupling parameters
> pcoupl          = no            ; Under NVT conditions pressure coupling is
> not done
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Google will turn up about 27 million posts with the same problem.  Please 
investigate the list archive (that's why it's there).

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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