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

[James Starlight]

The question in mdp options is here
gen_vel                  = no
gen_temp                 = 320
gen_seed                 = 473529


according to the central idea during equilibration I should to use
gen_vel                  = yes

to generate initial velocities ensemble.

however in that case simulation might not very stabile with parrinello
barostat. What is the better option here for martini equilibration7

Thanks!

James

2016-03-14 11:41 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> Ok, thanks!
>  I will put some additional questions in geeneral discussion!
> Salut Marseille! Last year I did pos-doc  in Nice- very nice place ç)
>
> A+
>
> J.
>
> 2016-03-14 11:34 GMT+01:00 Marlon Sidore <marlon.sidore at gmail.com>:
>> Yes, I am using the new-rf mdp options - and it seems to work nicely -
>> however I am not an expert.
>>
>> 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 11:31 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
>>>
>>> Thanks so much Marlon!
>>>
>>> Have you tried to run martini md for the membrane system7
>>>
>>> James
>>>
>>> 2016-03-14 11:06 GMT+01:00 Marlon Sidore <marlon.sidore at gmail.com>:
>>> > 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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>>