GROMACS version:2020.2
GROMACS modification: No
Dear gmx users,
I am a new one in MD and Gromacs, and I want to use the gmx to simulate the polymers with the Nose-Hoover thermostat as well as Parrinello-Rahman(PR). After the energy minimization finished(emtol<10), I got the error"step 0Segmentation fault (core dumped) ". In order to find the issue, I turn off the PR, it works well(NVT), and I also change the NH by V-rescale using PR, It also works well(NPT). I don’t know why the combination of NH and PR didn’t work well? My .mdp file is here:
; Run parameters
integrator = md-vv ;velocity verlet method
nsteps = 100000 ;
dt = 0.001 ; 1 fs
; Output control
nstxout = 1000 ;
nstvout = 1000 ;
nstenergy = 1000 ;
nstlog = 1000 ;
; Bond parameters
continuation = no
; Neighborsearching
cutoff-scheme = Verlet
nstlist = 20 ;
rcoulomb = 1.2 ;
rvdw = 1.2 ;
; Electrostatics
coulombtype = P3M-AD ;
fourierspacing = 0.16 ;
; Temperature coupling is on
tcoupl = nose-hoover ;
tc-grps = system
tau_t = 2.5 ;
ref_t = 1000 ;
nsttcouple = 100
; Pressure coupling is on
pcoupl = parrinello-rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
nstpcouple = 1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
gen_vel = no ; Velocity generation is off
I have tried to figure it out for several days but failed. Any suggestions will be greatly appreciated!
Thanks in advance!