[gmx-users] the density does not stablize

xiaowu759 xiaowu759 at qq.com
Thu Aug 4 11:34:04 CEST 2011


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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