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

[Antara mazumdar]

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.

 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

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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