[gmx-users] MD simullations with Morse potential

[fantasticqhl]

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!


All the best,

Qinghua



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