On 11/08/2011 10:22 PM, Da-Wei Li wrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error.
The reasons are
1. If I use .trr file instead of the low precision xtc file, things
become better, ie, I get much less snapshots that has high energy.
That doesn't make sense if the underlying frames are the same in your
.xtc and .trr files. However, if you're talking about different numbers
of frames, then you probably have transient periodicity artefacts.
2. I supplied -pforce in my mdrun -rerun and found that the high vdw
energy was usually caused by one pair of atoms, whose distance was
just very near the clash zone, so that small error on the coordinates
would cause large energy error. The force is always around 10000.
Sounds like you have a non-equilibrium trajectory (from your EM?), in
which case small deviations can have large effects.
3. Actually bond length and bond angle energies are also affected. I
can fully reproduce these two energies if I use .trr file in my rerun
but will get several tens of kj/mol error if I use .xtc file, for a
protein of size of 100 AA.
Several tens of kJ/mol error in the non-bonded energy looks OK compared
to the magnitude of the non-bonded energy. Anyway, if your purpose is to
compare energies computed from the same configurations, then you should
use the same configurations for computing the energies, not
approximations to those configurations.
Now the question I still have is whether numerical error can be so
large? The xtc file has a precision of 0.001 nm. Anyway, I will test
more by using double precision Gromacs and define energy groups so
that I can compare energy of protein directly between original MD and
rerun.
To Mark only
Thanks. Here it is my script for
rerun: mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
superpose: trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump
(em.tpr is generated for energy minimization, protein is in the middle
of the box)
Here you are generating a nojump trajectory file, but you are not doing
your rerun on it. That could explain some symptoms - you might not have
whole molecules.
Mark
rerun .mdp file:
**********************************************************
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 100 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 500000 ; save coordinates every 1000 ps
nstvout = 500000 ; save velocities every 1000 ps
nstxtcout = 5000 ; xtc compressed trajectory output every 1 ps
nstenergy = 5000 ; save energies every 1 ps
nstlog = 5000 ; update log file every 1 ps
xtc_grps = Protein ; save protein part only
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = hbonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 20 fs
rlist = 0.8 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = no ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = no ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = no ; 3-D PBC
; Dispersion correction
;DispCorr = EnerPres ; account for cut-off vdW scheme
DispCorr = no
; Velocity generation
gen_vel = no ; Velocity generation is off
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii = 1
rgbradii = 0.8
gb_epsilon_solvent = 80
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.25936
***************************************************************************************
Thanks all.
dawei
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