Dear gmxers,
I try to perform NPT MD to obtain the density of system. But the value of
density does not stablize even after over 40 ns. The content of mdp file can be
seen below. How to deal with it? Please give me some hints. Thanks a lot for
any replies.
.mdp file:
title =
cpp = /lib/cpp
include = -I../top
define = ;{-DFLEXIBLE,-DPOSRES}
integrator = md
dt = 0.001
comm_mode = Linear ;{Linear,Angular,No}
nstcomm = 10
nstcalcenergy = 1
nsttcouple = 1
nstpcouple = 1
comm_grps =
nsteps = 25000000
nstxout = 1000
nstvout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
ns_type = grid ;{simple,grid}
rlist = 1.0
coulombtype = pme
fourierspacing = 0.12 ; [0.12 nm]
optimize_fft = yes ;{no,yes}
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres ;{no,EnerPres,Ener}
pbc = xyz ; Periodic Boundary Conditions {xyz,no,xy}
tcoupl = berendsen ;no,berendsen,nose-hoover,v-rescale
tc-grps = Other
tau_t = 0.1
ref_t = 600
Pcoupl = berendsen ;{no,berendsen,Parrinello-Rahman}
Pcoupltype = isotropic ;{isotropic,semiisotropic;anisotropic;surface-tension}
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0 ;the unit is bar(1 bar =10^5 Pa)
gen_vel = no
gen_temp = 600
gen_seed = 173529
constraints = none ;{none,hbonds,all-bonds,h-angles,all-angles}
constraint_algorithm = LINCS ;{LINCS,SHAKE}
periodic_molecules = no ;{no,yes}
annealing = no ;{no,single,periodic}
annealing_npoints = 11
annealing_time = 0 100 200 300 400 500 600 700 800 900 1000
annealing_temp = 600 580 560 540 520 500 520 540 560 580 600
Best regards,
Dr. Chaofu Wu
------------------
Department of Chemistry and Materials Science
Hunan University of Humanities, Science and Technology,
Loudi 417000, the People's Republic of China (P.R. China)
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