[gmx-users] NPT equilibration

[Justin A. Lemkul]

shivangi nangia wrote:
> Hello,
> 
> 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?
> 

High temperature breaks down the water model and it, as you say, vaporizes.  NVT 
is often more suitable for high-temperature MD for this very reason.

-Justin

> Thanks,
> Shivangi
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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