[gmx-users] NVE mdp
Ramachandran G
gtrama at gmail.com
Thu Apr 1 09:46:39 CEST 2010
Dear Mark:
Thanks for your suggestions. I did equilibration for about 500ps but
still there is energy fluctuation exist (as give below). Is this deviation
is acceptable for NVE ensemble or still i need to equilibrate the system for
some more picosecond.
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Total-Energy -17710.5 66.1524 2.39547 -0.458016
-229.008
-----------------------
Rama
On Tue, Mar 30, 2010 at 11:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
>>
>> --
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