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

[David van der Spoel]

On 2010-07-10 15.56, zhongjin wrote:
> 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

Your position restraint force constant is so high that it will induce 
large fluctuations unless you use very short time steps.
What happens if you turn the position restraints off?
Or if you set the force constant to 1000 kJ/mol nm^2?

Normally the CNT should not deform even without position restraints, but 
you might need to use improper dihedrals with the right parameters 
(which I don't know, check the literature).

> -------------------------------------------------------------------------------
> 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
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se