Dear users:
I am simulating a CNT in water. In the energy minimization step, I
restrain the CNT by a constant 10e8,because I don't want the CNT to deform.
After minimization,the energy is -44054.835938. Then NVT and NPT equilibration
, at this step,the end C atoms are fixed by a constant 300000 to prevent from
being swept away. The temperature is OK. But the pressure may be not so
proper.It is larger than the set value.It is OK?
Energy Average RMSD Fluct. Drift Tot-Drift
-------------------------------------------------------------------------------
Pressure (bar) 1.5674 6891.48 6891.42 -0.100337 -100.337
the npt.mdp
title = OPLS Lysozyme NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = yes ; Restarting after NVT
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 cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; 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 = V-rescale ; modified Berendsen thermostat
tc-grps = CNT SOL ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; 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 = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
pressure
0.000000 -777.187622
0.200000 4527.866211
0.400000 -7984.377930
0.600000 5585.704102
0.800000 2807.166992
1.000000 -3545.817383
1.200000 4112.207031
1.400000 2340.378906
1.600000 -5803.378906
1.800000 8399.341797
2.000000 622.575745
2.200000 -3483.511963
2.400000 5920.053711
2.600000 -1108.013306
2.800000 -4201.218750
3.000000 5663.891602
3.200000 -4298.212402
3.400000 -1245.458862
.....
996.400024 -2921.789062
996.600037 3155.833008
996.800049 2046.963623
997.000061 -3057.696045
997.200073 2390.562500
997.400024 3122.586182
997.600037 -254.417053
997.800049 -741.921631
998.000061 -1757.483154
998.200073 -1241.035278
998.400024 15.855911
998.600037 316.152985
998.800049 1165.281250
999.000061 1776.868286
999.200073 55.826385
999.400024 538.847107
999.600037 4052.162842
999.800049 -6294.055664
1000.000061 -1811.536377
Thanks!
Zhongjin He
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