[gmx-users] NPT equilibration

[Deep Bhattacharya]

Thank you Mark.
So this pressure value that I am getting is normal correct?

Sincerely,
Deep

On Mon, Jul 11, 2016 at 2:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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-- 
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616