[gmx-users] NPT equilibration

[Mark Abraham]

Hi,

See http://www.gromacs.org/Documentation/Terminology/Pressure

Mark

On Mon, Jul 11, 2016 at 9:40 PM Deep Bhattacharya <hypergenetics at gmail.com>
wrote:

> Hello,
>
> I am have done NVT and NPT equilibration on my complex which is
> protein-carbohydrate solvent complex. I am getting -117.4 bar as my
> pressure after NPT.
> What could be a possible explanation to this?
> I have attached the NPT.mdp below
>
> title = PP
> define       =  -DPOSRES -DPOSRES_LIGAND; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 2500000 ; 0.001 * 2500000 = 2500 ps
> dt    = 0.001 ; 1 fs
> ; Output control
> nstxout = 0 ; save coordinates every 1.0 ps
> nstvout = 0 ; save velocities every 1.0 ps
> nstenergy = 0 ; save energies every 1.0 ps
> nstlog = 1
> nstxtcout   = 0
> energygrps  = Protein LIG
> ; 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         = 1        ;
> rcoulomb        = 0.8
> rvdw            = 0.8
> coulombtype     = Cut-off       ; Particle Mesh Ewald for long-
> vdwtype        = cut-off
> rlistlong      = 1.4
> epsilon-rf     = 61
> rlist          = 0.75
> ; Temperature coupling is on
> tcoupl = nose-hoover            ; modified Berendsen thermostat
> tc-grps       =Protein_LIG Water_and_ions   ; two coupling groups - more
> accurate
> tau_t = 2.0  2.0        ; 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        = 6.0            ; time constant, in ps
> ref_p        = 1.0            ; reference pressure, in bar
> compressibility     = 4.5e-5            ; isothermal compressibility of
> water, bar^-1
> refcoord_scaling    = com
> ; 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
>
> Please help.
> --
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
> --
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