On Jun 18, 2009, at 11:57 PM, Chih-Ying Lin wrote:
Hi
Here is my whole md.mdp.
But the final Temp = 303 K
No matter I extend the simulation time, the final Temp = 303 K and it
can not reach the ref_t = 300 K
Does it make sense?
Yes unfortunately the 303 K is what you should expect. This is
small deviation that results from some approximation made. This
is the best you can get. It is fine.
If you want you can play a bit with the cutoff options you have and
see the effect. For exemple you have a 9-1.4 nm twing-range
cutoff and you update every 5 steps. Reducing the update to 1
would certainly reduce the 303 closer to 300 K. And also reducing
1.4 to 1.2 nm should have the same effect. This is due to the
fact that you update the forces for atoms within 9-1.4 only every 5
steps.
check the literature and google on cutoff effect ... you'll find a lot
on it.
The simulation system is protein + ligand + counter ions.
ligand is the 33-atom molecule.
force field ffG45a3.
Thank you
Lin
; VARIOUS PREPROCESSING OPTIONS
title = Lysozyme
cpp = /lib/cpp
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for
integration
nsteps = 250000 ; 500 picoseconds total simulation
time
comm_mode = Linear ; Removing overall translations
from
the system
nstcomm = 1 ; ... and doing so every step
; OUTPUT CONTROL OPTIONS
nstxout = 1000 ; Writing full precision coordinates
every nanosecond
nstvout = 0 ; Writing velocities every nanosecond
nstfout = 0 ; Not writing forces
nstlog = 0 ; Writing to the log file every step
nstenergy = 1000 ; Writing out energy information
every step
nstxtcout = 1000 ; Writing coordinates every step
xtc_precision = 1000 ; Floating point number to integer
scaling
xtc-grps = System
energygrps = Protein Non-Protein
; NEIGHBORSEARCHING PARAMETERS
nstlist = 5
ns-type = Grid
pbc = xyz
rlist = 0.9
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 78
epsilon_r = 1
vdw-type = Cut-off
rvdw = 1.4
; Temperature coupling
Tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
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