[gmx-users] energy decreasing in NVE simulation
erikm at xray.bmc.uu.se
Wed May 19 21:50:52 CEST 2010
For more exotic NVE-systems I had to do some or several of the following
things to get stable Etot:
* have an even shorter timestep than one would expect from the applied
constraints and such.
* use double precision.
* apply the constraints with lower tolerance/more iterations etc.
Then there's a few things I notice in your setup:
* I see that you do not use constrints at all. I would give it a shot.
* Why do you have two separate comm-grps?
Yun-an Yan skrev:
> Dear all,
> When I try to simulation with NVE ensemble, the
> total energy keeps decreasing. Geometry optimization
> and solvent equilibration are done before the NVE simulation.
> I follow the requirements provided in
> Would any one help me to figure out what was wrong with
> my settings?
> Millions of thanks and best wishes,
> BTW: Please check the following for the .mdp file
> ;Run control: A leap-frog algorithm for integrating Newton's equations.
> integrator = md
> ;time step in femtoseconds
> dt = 0.001
> ;number of steps
> nsteps = 10000000
> ;No constraints
> constraints = none
> constraint_algorithm = shake
> shake_tol = 1e-08
> ; group(s) for center of mass motion removal
> comm-grps = AA CCl4
> ; frequency for center of mass motion removal
> nstcomm = 1000
> ;frequency to write coordinates to output trajectory file
> nstxout = 1000
> ;frequency to write velocities to output trajectory file
> nstvout = 1000
> ;frequency to write energies to log file
> nstlog = 1000
> ;frequency to write energies to energy file
> nstenergy = 1000
> ;group(s) to write to energy file
> energygrps = System
> ;Frequency to update the neighbor list (and the long-range forces,
> ;when using twin-range cut-off's).
> nstlist = 10
> ns_type = grid
> rlist = 1.5
> ; Use periodic boundary conditions in all directions.
> pbc = xyz
> ;cut-off distance for the short-range neighbor list
> ;treatment of electrostatic interactions
> coulombtype = PME-switch
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> rcoulomb_switch = 1.0
> rcoulomb = 1.2
> ;treatment of van der waals interactions
> vdwtype = Switch
> rvdw-switch = 1.0
> rvdw = 1.2
> dispcorr = EnerPres
> ;Temperature coupling
> tcoupl = no
> ;Pressure coupling
> pcoupl = no
> ;Velocity generation
> gen_vel = no
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/
More information about the gromacs.org_gmx-users