[gmx-users] the density does not stablize

[Mark Abraham]

On 04/08/11, xiaowu759  <xiaowu759 at qq.com> wrote:
> 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.
> 
> 

We have no idea whether your judgement that density is not stabilized after 40ns is sound, because you provided no data. Your temperature coupling is to group "Other", which may or may not be reasonable. Your integration time step is possibly too large for a simulation using no bond constraints. Your initial density could be so far from correct that reaching equilibrium is infeasible. You'll need to provide a lot more information to get useful help.

Mark


> 
> 
>  
> 
> .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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