[gmx-users] Re: NPT equilibration

[Vitaly Chaban]

> I am having problems in carrying out a NPT equilibration of my system at 500
> K.
>
> System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid
> anion.
>
> NVT equilibration gives expected results.
>
> When I load the npt.gro file in VMD, its seems as if the molecules have
> fragmented/vaporized.
>
> nvt.mdp:
>
> title    = hist NPT equilibration
> define      = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md     ; leap-frog integrator
> nsteps      = 50000     ; 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 cells
> 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     = Protein Non-Protein   ; two coupling groups - more accurate
> tau_t    = 0.1 0.1   ; time constant, in ps
> ref_t    = 500    500   ; 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
>
>
> If I use the same exact system and run NVT and NPT equilibration at 300 K,
> everything seems to be working.
>
> What could be going wrong at 500 K?
>
> Thanks,
> Shivangi



Hi Shivangi,

Why do you think that this physical system should not vaporize before
500K? At least, waters are certain to fly away.

If 500K is needed only for faster relaxation, just use NVT, and then
gradually cool the system to its liquid state.

Good luck!

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216