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

[XAvier Periole]

It is a bit difficult to guess what is exactly happening. Your  
starting structure
seem to be the problem, but your topology could also be partly  
responsible.

One easy thing to do is the decrease your time step to 0.0001 which  
would
decrease the chances that your system explodes.

Also try to work on refining your non-bonded set-up, it looks like you  
use
straight and short cut-offs.

XAvier.

On Mar 19, 2009, at 6:14 AM, Pawan Kumar wrote:

> 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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