[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Mark Abraham]

Hi,

On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <antara.mazumdar at igib.in>
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. The lincs warning error is coming from BB and SC1
> atoms of one of the protein residues.
>

There are lots of possible places to go wrong, including not making your
production .tpr based on the outputs of your equilibration. This seems
quite a likely possibility.

You should also consider further equilibration - whether using Martini or
not, it is sometimes necessary to use a small time step when relaxing
problem configurations.


>  But on the contrary, it runs on the desktop successfully. *My production
> run mdp file details are below :*
>
>
> .
>
> This is the MD.mdp file :ntegrator               = md
> tinit                    = 0.0
> dt                       = 0.020
> nsteps                   = 2500000000
>
> nstxout                  = 2000
> nstvout                  = 2000
> nstfout                  = 2000
> nstlog                   = 2000
> nstenergy                = 2000
> nstxtcout                = 2000
> xtc_precision            = 100
>
> ns_type                  = grid
> pbc                      = xyz
> nstlist                 = 10
> cutoff-scheme           = Verlet
> rlist                   = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = none
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
>
> tcoupl                   = v-rescale
> tc-grps                  = protein CHOL_POPC_DPSM_DPCE W_ION
>
> tau_t                    = 1.0 1.0  1.0
> ref_t                    = 303.15 303.15 303.15
>
> ; Pressure coupling:
> Pcoupl                   = berendsen
> Pcoupltype               = semiisotropic
> tau_p                    = 5.0  5.0
> compressibility          = 3e-4 3e-4
> ref_p                    = 1.0  1.0
> ; GENERATE VELOCITIES FOR STARTUP RUN:
> gen_vel                  = no
> refcoord_scaling         = all
>
> *the command used for mdrun :*
>
> -deffnm MD -pin on -rdd 1.8 -np 16
>

mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
Please don't edit and filture things, copy and paste whole actual things.
:-)

Mark

I would also like to mention that i generated the initial structure of the
> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
> have followed the exact builder protocol for the equilibration and
> minimisation.
>
> Kindly suggest something!
>
> Thanks,
> Antara
>
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