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?
Erik Marklund
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
http://www.gromacs.org/Documentation/Terminology/NVE
Would any one help me to figure out what was wrong with
my settings?
Millions of thanks and best wishes,
Yun-an
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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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