[gmx-users] Re: the Pressure control in GROMACS 4.0.7

[zhongjin]

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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