[gmx-users] NVE mdp

[Erik Marklund]

Mark Abraham skrev:
> 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!
The system is neither coupled to a thermostsat nor to a barostat, and 
the number of particles are constant. Ideally the total energy would be 
constant, since any initial "imbalance" between kinetic and potential 
energy in such a system would only lead to a repartitioning of named 
energies over time. This in turn would cause a change in temperature, 
but not in total energy.

My guess is that the constraints acts as an energy sink, and my advice 
is to tune down the shake tolerance, or to use likns with higher values 
for order and iter than the default values. Also, runnig your simulation 
in double precision may help.

/Erik
>
>> 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
>>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/