[gmx-users] Alanine dipeptide simulations

[Sai Pooja]

Hi,

I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator               = md
dt                       = 0.002
nsteps                   = 500000

; OUTPUT CONTROL OPTIONS
nstxout                  = 0                    ; No output, except for last
frame (coordinates)
nstvout                  = 0                    ; No output, except for last
frame (velocities)
nstfout                  = 0                    ; No output, except for last
frame (forces)
nstlog                   = 5000                ; Write every step to the log
nstenergy                = 5000                    ; Write energies at every
step
xtc_grps                 = Protein SOL
nstxtcout                = 5000                    ; Do not write a
compressed trajectory
energygrps               = Protein SOL  ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = PME
fourierspacing           = 0.15
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                     = 1.0

; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no
; Temperature coupling
tcoupl                   = nose-hoover
tc-grps                  = Protein  Non-Protein
tau_t                    = 0.2      0.2
ref_t                    = 300      300

; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; OPTIONS FOR BONDS
constraints              = all-bonds


Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.
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