In God We Trust
Hello Dear GMX users
I want to do MD on one peptide in water with gromacs 4.5.3.
I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I
do final mdrun it has load imbalance and when I try -pd option it stops
after 265 ps without any error massage !, can everybody help me.
Here is my mdp file .
constraints = hbonds
integrator = md
dt = 0.002
nsteps = 50000000
nstcomm = 10
comm_mode = Linear
comm_grps = protein
nstxout = 250
nstvout = 1000
nstfout = 0
nstcalcenergy = 10
nstlog = 1000
nstenergy = 1000
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
energygrps = protein SOL
; Berendsen temperature coupling is on in three groups
Tcoupl = v-rescale
tau_t = 0.1 1
tc-grps = protein bulk
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-Rahman
tau_p = 1
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Many thanks in advance for your help and your reply.
Yours truly
Karim Mahnam
Institute of Biochemistry and Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/
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