[gmx-users] NVE mdp

[Mark Abraham]

On 31/03/2010 2:51 PM, Ramachandran G wrote:
> Dear gromacs users:
>           I am using following mdp file as input for simulating the
> system with NVE ensemble. But when i check the 'Total energy',
> it doesn't seems to remain constant and keep decreasing. I am also

Thus, you are not yet in an NVE ensemble. Generating velocities is only 
an approximate process, and it takes at least several picoseconds for 
some observables to start converging to their ensemble-average values. 
So, equilibrate before you start collecting data!

> giving some part of my output. Thanks for your help
> Rama
>
> title                = Water box
> DEFINE               = -DFLEXIBLE
> constraints          = hbonds
> constraint_algorithm = shake

Don't simulate with flexible water and bond constraints. It's inconsistent.

Mark

> integrator         = md
> dt                 = 0.001   ;
> nsteps             = 1500000  ;
> nstcomm            = 100
> nstlist            = 10
> ns_type            = grid
> nstenergy          = 5
> nstlog             = 0
> nstvout            = 5
> nstxout            = 5
> nstxtcout         = 0
> xtc-precision      = 100
> nstfout            = 0
> coulombtype        = shift
> fourierspacing     = 0.135
> pme_order          = 4
> vdwtype            = switch
> rvdw               = 1.0
> rlist              = 1.2
> rcoulomb           = 1.0
> pbc                = xyz
> fourier_nx      = 0.0
> fourier_ny      = 0.0
> fourier_nz      = 0.0
> ;Berendsen temperature coupling is on
>
> Tcoupl          = no   ; temperature bath (yes, no)
> tau_t           = 0.1
> tc-grps         = system
> ref_t           = 200
>
> ;Berendsen Pressure coupling is on
> pcoupl          = no         ; pressure bath (yes, no)
> pcoupltype      = isotropic
> tau_p           = 0.5
> compressibility = 4.5e-05
> ref_p           = 1.0
>
> ;Generate velocities is on at 300K
> gen_vel         = yes       ; generate initial velocities
> gen_temp        = 300.0     ; initial temperature
> gen_seed        = 173529    ; random seed
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> Output:
> "Total Energy"
>      0.000000  -59821.300781
>      0.005000  -59806.011719
>      0.010000  -59790.937500
>      0.015000  -59799.031250
>      0.020000  -59803.445312
>      0.025000  -59799.058594
>      0.030000  -59803.445312
>      0.035000  -59804.835938
>      0.040000  -59801.652344
>      0.045000  -59803.144531
>      0.050000  -59804.605469
>      0.055000  -59803.421875
>      0.060000  -59806.074219
>      0.065000  -59805.125000
>      0.070000  -59803.632812
>      0.075000  -59805.742188
>      0.080000  -59807.140625
>      0.085000  -59806.539062
>      0.090000  -59806.328125
>      0.095000  -59806.949219
>      0.100000  -59807.351562
>      0.105000  -59806.531250
>      0.110000  -59806.894531
>      0.115000  -59808.933594
>      0.120000  -59808.585938
>      0.125000  -59807.019531
>      0.130000  -59808.171875
>      0.135000  -59809.117188
>      0.140000  -59808.242188
>      0.145000  -59808.820312
>      0.150000  -59808.750000
>      0.155000  -59806.507812
>      0.160000  -59808.839844
>      0.165000  -59810.800781
>