[gmx-users] regarding nvt

[Peter C. Lai]

What is the output for the temperatures of the Proten and Non-Protein
you get from g_energy?

On 2012-01-06 04:45:05PM +0530, priya thiyagarajan wrote:
> hello sir,
>  sorry i left few lines while pasting my nvt.mdp input file
>  thi is my nvt.mdp file
> 
> 
> title           =GROMOS43a1 lipopeptide NVT equilibration
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 100000                ; 2 * 100000 = 200 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1     ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = No    ; modified Berendsen thermostat
> tc-grps         = DRG   SOL     ; two coupling groups - more accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each
> group, in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
> 
> 
> i am not getting equilibrium temperature even after my nvt step
> 
> 
> help me with your answer..
> 
> Thanking you,

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-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
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