[gmx-users] Membrane Equilibration

Neha nshafique at wesleyan.edu
Tue Jun 11 17:22:43 CEST 2013

Hi everybody,

I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
coupling. However, I read that Parinello-Rahman is not great for
equilibration so I thought I would do a small run using the Berendsen
barostat to decrease the chances of large oscillations. I then used the .gro
file obtained from that run to start a new run using Parrinello-Rahman. I am
not sure if that's the correct way to go about doing what I want to do.

My Parrinello run also terminated a little while in, with the error that 2
of my atoms have moved further apart than the cut-off distance. A part of my
mdp file is pasted below and I was wondering if anyone had any suggestions
as to stop that from happening. My time step is 0.02 ps and I thought
increasing tau-p might work. I am using the compressibility from the map
file on the Martini website and am worried that might be too large. Any help
will be super useful! Let me know if you need any more information.

; Temperature coupling   =
tcoupl                   = nose-hoover
; Groups to couple separately =
tc-grps                  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0 1.0
ref_t                    = 320 320
nsttcouple               = 1
; Pressure coupling      =
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 5.0  5.0
compressibility          = 3e-4 3e-4
ref_p                    = 0.0  0.0
nstpcouple               = 5

gen_vel                  = yes
gen_temp                 = 105
gen_seed                 = 473529

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