[gmx-users] Doubt regarding membrane protein in POPC bilayer

[Pawan Kumar]

Dear gmx-users,

Greetings from Pawan.
I have modelled the structure of a protein using Modeller and then energy
minimized using gromacs.
Then I used the popc128a bilayer from Tieleman sir's website for inserting
the protein.
I created a bigger bilayer using the genconf command in gromacs.
I was able to minimize the bigger bilayer and then inserted my protein in
the bilayer using the genbox command in gromacs.
I was able to minimize the system.
But when I tried to do an mdrun for few steps restraining the protein I
ended with errors like :
1) pressure scaling more than 1%
2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation.
3) too many lincs warnings.
4) Number of grid cells is zero. probably the system and the box collapsed.

I tried to solve these errors by increasing the tau_p value for pressure
scaling error and higher table-extension value for the 1-4 interaction
warning in the mdp file but nothing is working out.
I have given the mdp files at the end for reference.
Please give me some suggestions as how to continue further.

For energy minimization:
------------------------------------
title               =  Protein in POPC bilayer
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
integrator          =  steep
nsteps              =  50000

; Constrain control
constraints         =  none

; Output frequency for coords (x), velocities (v) and forces (f)
nstxout             =  100
nstvout             =  100
nstfout             =  100

; nblist update frequency
nstlist             =  10

; ns algorithm
ns_type             =  grid
rlist               =  1

; Method for doing VdW
vdw-type            =  Cut-off
rvdw                =  1

; Method for doing electrostatics
coulombtype        =  Cut-off
rcoulomb            =  1

; Center of mass control
nstcomm              =  1

; Periodic boundary conditions
pbc                  =  xyz

; Mode for center of mass motion removal
comm-mode            =  Linear

;       Energy minimizing stuff
emtol                =  2250
emstep               =  0.001


For mdrun using position restraints:
---------------------------------------------------
title               =  Protein in POPC
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000    ; total 10 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps            =  Protein    Non-Protein
tau_t               =  0.1    0.1
ref_t               =  300    300
; Energy monitoring
energygrps        =  Protein    Non-Protein
; Pressure coupling is not on
Pcoupl              =  berendsen
tau_p               =  5.0 5.0
compressibility     =  4.5e-5 4.5e-5
ref_p               =  1.0 1.0
Pcoupl_type         =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

Thanking you,

Yours sincerely,
Pawan
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