From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Jun 16 2005 - 10:30:28 CDT
The energy drift observed in your simulations is probably caused by the
time steps you are using. If you want to have a very good energy
conservation, a *uniform* 1 femtosecond time step should work (you could
also try 2 fs with nonbondFreq 1, fullElectFrequency 1 and rigidBonds).
PS: Good references about energy conservation and use of multiple timestep
 Nonlinear Resonance Artifacts in Molecular Dynamics Simulations. T.
Schlick, M. Mandziuk, R. D. Skeel and K. Srinivas. J. Comput. Phys.,
 Verlet-I/r-RESPA Is Limited by Nonlinear Instability. Q. Ma, J.
Izaguirre, and R. D. Skeel. SIAM J. Sci. Comput., 24(6), 1951-1973, 2003
 Difficulties with Multiple Timestepping and the Fast Multipole
Algorithm in Molecular Dynamics. T. Bishop and Robert D. Skeel and K.
Schulten. J. Comp. Chem., 18(14):1785-1791, 1997.
 Langevin Stabilization of Molecular Dynamics J. A. Izaguirre, D. P.
Catarello, J. M. Wozniak, and R. D. Skeel. J. Chem. Phys., 114(4),
On Wed, 15 Jun 2005, [ISO-8859-1] Leonardo Sepulveda Durán wrote:
> Hello everybody
> I was trying to do a NVE simulation in NAMD. I used imput coordinate
> and velocity files from a NVT simulation which was equilibrated at
> desired temperature (498 K)
> Looking at TOTE3, it is obvious my system's energy underwent a slow
> drift (from -20235 to -20225 in 250 ps ). The .conf I used is below:
> structure ./ubq-wb.psf
> coordinates ./ubq-min.coor
> # For Continuing a run, otherwise comment all but firsttimestep
> set inputname ubq-heat
> binCoordinates $inputname.coor ;# coordinates for last run (binary))
> binVelocities $inputname.vel ;# velocities for last run (binary)
> extendedSystem $inputname.xsc ;# Cell dymentions for last run
> firsttimestep 41500 ;# Last step previous run
> numsteps 125000 ;# run stops when this
> step is reached
> # Force-Field Parameters
> paraTypeCharmm on
> parameters /home/RPMs/NAMD/toppar/par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 10.; # cutoff-2
> cutoff 12.; # may be 10 with PME
> pairlistdist 14.; # cutoff+2
> margin 0.498;
> # Integrator Parameters
> timestep 2.0; # 2fs/step
> rigidBonds all; # needed for 2fs steps (SHAKE)
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> outputPairlists 1000
> # Periodic Boundary Conditions
> cellBasisVector1 50.68 0. 0.
> cellBasisVector2 0. 52.37 0.
> cellBasisVector3 0. 0. 56.27
> cellOrigin 30.85 29.14 17.90
> wrapAll on
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 54
> PMEGridSizeY 54
> PMEGridSizeZ 60
> # Output
> outputName ubq-eq
> binaryOutput yes;
> restartfreq 500; # 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
> outputTiming 1000
> I was wondering if someone can give me an advice about how to get my
> simulations conservative. I am confused about some concepts and
> parameters...for example, in the manual, stepspercycle is explained
> as the number of timesteps beetween atom
> reasignments; I thought it was refering to pairlist reasignment, but
> later "pairlistpercycle" is defined as the number of times pairlists
> are regenerated in one cycle...so if I have
> stepspercycle = 20
> pairlistpercycle = 2
> is the same as using
> stepspercycle = 10
> pairlistpercycle = 1 ?????
> I really dont understand the difference. Also I put outputPairlists
> because it sound useful to avoid atoms to pass the pairlist boundary,
> but i am not sure if only give the pairlists violations. So I would
> like to ask if someone have done NVE simulations succesfully, and what
> parameters can be adecuate to do it.
> PD: I attach a .pdf with temperature and energy from my simulation.
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