[gmx-users] MD simullations with Morse potential

[Justin Lemkul]

On 4/25/14, 10:00 AM, fantasticqhl wrote:
> Dear All,
>
>
> I am trying to do a simulations with morse potential for bonds, I can do the
> minimization of the system, but I can not do the MD optimization without
> lincs constraints on bonds since using Morse potential with constraints is
> useless.
>
> The error was shown as "Segmentation fault (core dumped)" , I did not found
> some other information in the log file. The system was well minimized before
> doing md optimization. Here is my mdp file:
>
> ######################
> title           = OPLS Lysozyme NPT equilibration
> ;define          = -DPOSRES          ; position restrain the protein
> ; Run parameters
> integrator           = md                      ; leap-frog integrator
> nsteps               = 100000                ; 2 * 50000 = 100 ps
> dt                      = 0.0005                ; 2 fs
> ; Output control
> nstxout               = 2500            ; save coordinates every 0.2 ps
> nstvout                = 2500            ; save velocities every 0.2 ps
> nstenergy            = 2500          ; save energies every 0.2 ps
> nstlog                 = 2500             ; update log file every 0.2 ps
> ; Bond parameters
> continuation        = no                             ; Restarting after NVT
> ;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                    = 1.2                              ; short-range
> neighborlist cutoff (in nm)
> rcoulomb            = 1.2                           ; short-range
> electrostatic cutoff (in nm)
> rvdw                   = 1.2                          ; 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              = Protein Non-Protein                               ;
> 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 on
> pcoupl              = Parrinello-Rahman                                    ;
> Pressure coupling on in NPT
> pcoupltype        = isotropic
> ; uniform scaling of box vectors
> tau_p               = 2.0
> ; time constant, in ps
> ref_p                = 1.0
> ; reference pressure, in bar
> compressibility = 4.5e-5                                                 ;
> isothermal compressibility of water, bar^-1
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc                  = xyz
> ; 3-D PBC
> ; Dispersion correction
> DispCorr          = EnerPres
> ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel            = yes
> ; Velocity generation is off
> gen_temp        = 300
> ; temperature for Maxwell distribution
> gen_seed        = 173529
> ; generate a random seed
> morse             = yes
>
> ####################################
>
> Is there some special rule for md simulations with morse potential? But I
> did not found it in the manual. Could someone give some suggestions? Any
> response will be highly appreciated!
>

The first problem I suspect is the use of the Parrinello-Rahman barostat while 
generating velocities.  That combination often results in instability for any 
system.  Try NVT equilibration before moving to NPT.

-Justin

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

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

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
http://mackerell.umaryland.edu/~jalemkul

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