[gmx-users] Simulation of the membrane protein using Martini. MDP options

James Starlight jmsstarlight at gmail.com
Mon Mar 14 11:01:46 CET 2016


I am trying to use MARTINI ff for simulation of membrane protein.

Two questions regarding mdp options for such runs

1) May I use below options taken from the Justin tutorial with the MARTINI ff

; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5    ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4    ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT

2) is it possible to start equilibtation run with the applied
Parrinello barostat (skipping NVT phase) using bigger taup due to the
coarse graining of the system 7

Thanks so much for help!!


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