[gmx-users] MD simullations with Morse potential

[fantasticqhl]

Hello Tsjerk,


Thanks very much for your asking! No, I can't run the NVT equilibration 
with morse potential for bonds, even for a solvated three-residue system 
(Gly-Ser-Asn, 2601 atoms in total ).


Here is the NVT mdp file:

################################################
;define                  = -DPOSRES                      ; position 
restrain the protein
; Run parameters
integrator             = md                                   ; 
leap-frog integrator
nsteps                   = 100000                            ; 2 * 50000 
= 100 ps
dt                          = 0.001     ; 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 ; 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                    = 1 ; 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)
vdwtype                = cut-off
; Electrostatics
coulombtype        = pme                                   ; Particle 
Mesh Ewald for long-range electrostatics
pme_order           = 4                                     ; cubic 
interpolation
fourierspacing      = 0.12                                  ; 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 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             = 173529                                    ; 
generate a random seed
morse                 = yes

###############################################


The error is still the segmentation fault. I believe it is not the 
problem of my system since it is such a small system.

Does morse potential work for you? Thanks very much!


All the best,
Qinghua





On 04/26/2014 06:55 AM, Tsjerk Wassenaar [via GROMACS] wrote:
> Hi Qinghua,
>
> Can you run NVT equilibration? Does it work with nstlist set to 1?
>
> Cheers,
>
> Tsjerk



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