[gmx-users] Semiisotropic pressure coupling

[shivangi nangia]

Hello All,

I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG
using the script provided by Tsjerk)
The system consists of popc, 21 AA protein, water and ions.

After reverse CG I did short EM and 5 ns NVT simulation.
However, when I do NPT simulation, the area per lipid drops from 67 ang2 to
57 within 1 ns ( x and y dimensions decrese and z increases).

I am using semiisotropic pressure coupling.

I have a question regarding that.
I noticed in example .mdps and the tutorial by Justin Lemkul

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp


tau_p is specified, the ref_p and compresibility is same, does not that
mean essentially I am doing isotropic coupling?

I am confused what values should be used.

Please suggest.

Thanks,
sxn




*md.mdp:*
; RUN CONTROL PARAMETERS

dt                       = 0.002
;nsTEPS                   = 12500000 ;25ns
nsTEPS                   = 25000000 ;50ns

integrator             = md
ld-seed                 = -1

; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 10


; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 50000
nstvout                  = 50000
energygrps               = Protein     Non-Protein
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstcalcenergy            = -1
nstenergy                = 100

nstxtcout                = 500
xtc-precision            = 1000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 1
rlist
; ns algorithm (simple or grid)
ns-type                  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic_molecules       = no
; nblist cut-off
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.2
fourierspacing           = 0.16
pme_order                = 4
optimize-fft            = yes
; Method for doing Van der Waals
vdw-type                 = switch
; cut-off lengths
rvdw-switch              = 1.0
rvdw                     = 1.2

; OPTIONS FOR BONDS
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = Lincs
lincs-order             = 6
; temperature controls
tcoupl                  = v-rescale
tc-grps                 = Protein       Non-Protein
tau-t                   = 1.0   1.0
ref-t                   = 303    303

; Pressure Controls
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau-p                   = 1.0
ref-p                   = 1.0 1.0
compressibility         = 4.5e-5 4.5e-5