GROMACS version:4.5
GROMACS modification: No
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Hi,
I am a new user of Gromacs. When I try to do MD of membrane protein with a POPC bilayer. The results are strange. Many lipid molecule were stretched to a straight line in the box. The equilibration results seems right. Below is the mdp parameters, which is from CHARMM GUI prepared files, just changed nsteps. Does anyone know what the problem is. Thanks in advance.
integrator = md
dt = 0.002
nsteps = 100000000
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
tcoupl = Nose-Hoover
tc_grps = SOLU MEMB SOLV
tau_t = 1.0 1.0 1.0
ref_t = 303.15 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU_MEMB SOLV