[gmx-users] Cannot get correct pressure value with MTTK pressure coupling
Bao Kai
paeanball at gmail.com
Wed Jun 6 17:07:45 CEST 2012
HI, all,
I want to use MTTK for the pressure coupling for NPT simulation, while
I can not get the correct pressure value.
The following result is a simulation with 1000 SPC-E water molecules
with temperature 303.15K and pressure 1 bar.
Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets
All statistics are over 200001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 303.155 0.016 5.54033 0.0532334 (K)
Pressure 138.295 1.3 429.699 -5.68756 (bar)
Density 1002.82 0.24 8.04912 0.668867 (kg/m^3)
.
The following is the mdp file
title = fizzy water
; Run parameters
integrator = md-vv ; velocity-verlet integrator
nsteps = 1000000; 0.001 * 1000000 = 1000 ps, 1 ns
dt = 0.001 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps. Incr by *10
nstvout = 1000 ; save velocities every 2 ps. Incr by *10
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps. Incr by *10
nstenergy = 1000 ; save energies every 2 ps. Incr by *10
nstlog = 1000 ; update log file every 2 ps. Incr by *10
; Bond parameters
continuation = yes ; <-- Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; 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 cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
rvdw = 0.9 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 303.15 ; reference temperature, one for each group, in K
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; turning on pressure coupling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; <-- Pressure coupling is on
pcoupl = mttk; Pressure coupling on in NPT
nstpcouple = 1;
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 = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; <-- Velocity generation is off
;
Could anybody tell me anything wrong with my configuration?
Thank you very much.
Best Regards,
Kai
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