[gmx-users] unusual error in Gromacs

[Justin Lemkul]

On 3/24/15 9:39 AM, soumadwip ghosh wrote:
> Dear users,
>                   I was trying to equilibrate my system containing a ssDNA,
> CNT, water and some ions. I observed that it took many steps for the energy
> minimization of the system and after 7/8 steps the potential finally
> converged < 500 steps in a steepest descent method. Now, with that system I
> proceeded to NVT equilibration. Initially, by keeping the dt= 0.002 an
> error saying that
>
> 'A charged group moved too far between two domain decomposition steps'
>
> Then I decreased the dt to 0.001 and finally to 0.0005 and tried to
> equilibrate the system at NVT first for 200 ps and then for 1 ns and 2 ns
> respectively. The temp of the system got converged nicely. Now, when I
> increased the dt to 0.001 while running mdrun I'm getting this error-
>
> Program mdrun, VERSION 4.5.6
> Source code file: ../../include/vec.h, line: 765
>
> Fatal error:
> Can not invert matrix, determinant =
>
> Then I went back to the dt = 0.0005 and tried to do mdrun but again this
> error occured. It is reported as a bug somewhere on the internet but I dont
> know how to fix this. As you can see I am having problems with a simple NVT
> equilibration and cant proceed further. Is it really a bug or is it
> appearing because my system is not well-equilibrated? Any suggestion would
> be of great relief. I am pasting my NVT.mdp file below for your reference.
> Any general guidance regarding the handling of the particular error or the
> overall equilibration will be greatly appreciated.
>
>
> title           = OPLS Lysozyme NVT equilibration
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 2000000               ; 2 * 500000 = 1000 ps
> dt              = 0.001         ; 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
> ;
> freezegrps = 1MY0
> freezedim =  Y Y Y
> ; 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           = 1.5           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.5           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.5           ; 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 is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tC-GRPS         = SYSTEM                ; 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 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
>
>
> I changed the dt as required and this 1MYO is my CNT. Thanks for your time.
>

All of the above errors are indicative of generic failure.

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

-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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