On 11/20/12 12:29 PM, tarak karmakar wrote:
Thanks Justin for the quick reply.
Is there any problem with the algorithms ??
I have used Velocity Verlet , Nose-Hoover and MTTK combination. SHAKE
has been used to constrains the H-covalent bonds.
tau_t = 1 ps
tau_P = 1 ps
I got the mean pressure at ~130 bar.
Previously with the same initial coordinates I have used Leap-Frog,
NH, Parinello-Rehman with LINCS to constrain H-covalent bonds.
tau_t was 0.1 ps
and tau P was 2 ps.
The I have seen the pressure fluctuating around 1 bar( as expected)
So can you please inform me from where this problem is coming -
algorithms and/ tau_t and tau_P parameters ?
I have no personal experience with the md-vv/MTTK combination. The way to test
if there is a bug or something is to take an equilibrated system (as suggested
before) and continue it with the desired parameters. If they deviate or
incorrectly report pressure, then there's probably a bug. I'm not ready to
conclude that until it is tested though.
-Justin
On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/20/12 11:26 AM, tarak karmakar wrote:
Dear All,
I want to keep the pressure at 1.0 bar during the NPT simulation. But
it is fluctuating around 130 bar. So can anyone please inform me
whether I have missed any keyword in my .mdp file OR is it because of
the tau_p which I set 1s 1.0 ps.
Equilibrate with a weak coupling method (Berendsen) and then proceed using
better algorithms.
-Justin
Thanks
The .mdp file is given below
; 7.3.3 Run Control
integrator = md-vv ; md integrator
tinit = 0 ; [ps] starting time for
run
dt = 0.001 ; [ps] time step for
integration
nsteps = 15000000 ; maximum number of
steps to integrate, 0.001 * 15,00,000 = 15 ns
nstcomm = 1 ; [steps] frequency of
mass motion removal
comm_grps = Protein Non-Protein ; group(s) for center
of mass motion removal
; 7.3.8 Output Control
nstxout = 10000 ; [steps] freq to write
coordinates to trajectory
nstvout = 10000 ; [steps] freq to write
velocities to trajectory
nstfout = 10000 ; [steps] freq to write forces
to trajectory
nstlog = 1000 ; [steps] freq to write
energies to log file
nstenergy = 1000 ; [steps] freq to write
energies to energy file
nstxtcout = 1000 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 1000 ; [real] precision to write
xtc trajectory
xtc_grps = System ; group(s) to write to xtc
trajectory
energygrps = System ; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions
in all directions
rlist = 1.2 ; [nm] cut-off distance for
the short-range neighbor list
nsttcouple = 1
nstpcouple = 1
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald
electrostatics
rcoulomb = 1.2 ; [nm] distance for Coulomb
cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw = 1.2 ; [nm] distance for LJ cut-off
DispCorr = EnerPres ; apply long range dispersion
corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.12 ; [nm] grid spacing for FFT
grid when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = Nose-Hoover ; Nose-Hoover
temperature coupling
tc_grps = Protein Non-Protein ; groups to
couple seperately to temperature bath
tau_t = 1.0 1.0 ; [ps] time
constant for coupling
ref_t = 300 300 ; [K]
reference temperature for coupling
; 7.3.15 Pressure Coupling
pcoupl = MTTK ; pressure coupling
where box vectors are variable
pcoupltype = isotropic ; pressure coupling in
x-y-z directions
tau_p = 1.0 ; [ps] time constant
for coupling
compressibility = 4.5e-5 ; [bar^-1] compressibility
ref_p = 1.0 ; [bar] reference
pressure for coupling
; 7.3.17 Velocity Generation
gen_vel = no ; velocity generation turned off
; 7.3.18 Bonds
constraints = h-bonds
constraint_algorithm = SHAKE ; SHAKE Constraint Solver
shake_tol = 1.0e-5
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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