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

[Marlon Sidore]

Hi,

If you're using Gromacs 5.x, I suggest using the mdp options from these
files:
http://md.chem.rug.nl/index.php/mdp5

The paper associated with these is here:
http://www.sciencedirect.com/science/article/pii/S0010465515003628

Best regards

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-03-14 11:01 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:

> Hi,
>
> 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!!
>
> James
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