Dear gmx-users,<br><br>Greetings from Pawan.<br>I have modelled the structure of a protein using Modeller and then energy minimized using gromacs.<br>
Then I used the popc128a bilayer from Tieleman sir's website for inserting the protein.<br>I created a bigger bilayer using the genconf command in gromacs.<br>I was able to minimize the bigger bilayer and then inserted my protein in the bilayer using the genbox command in gromacs.<br>
I was able to minimize the system.<br>
But when I tried to do an mdrun for few steps restraining the protein I ended with errors like : <br>1) pressure scaling more than 1%<br>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<br>
These are ignored for the rest of the simulation.<br>3) too many lincs warnings.<br>4) Number of grid cells is zero. probably the system and the box collapsed.<br><br>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.<br>I have given the mdp files at the end for reference.<br>
Please give me some suggestions as how to continue further.<br><br>For energy minimization:<br>------------------------------------<br>title = Protein in POPC bilayer<br>cpp = /usr/bin/cpp<br>
define = -DFLEXIBLE<br>integrator = steep<br>nsteps = 50000<br><br>; Constrain control<br>constraints = none<br><br>; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 100<br>nstvout = 100<br>nstfout = 100<br><br>; nblist update frequency<br>nstlist = 10 <br><br>; ns algorithm <br>ns_type = grid<br>rlist = 1<br>
<br>; Method for doing VdW <br>vdw-type = Cut-off<br>rvdw = 1<br><br>; Method for doing electrostatics <br>coulombtype = Cut-off<br>rcoulomb = 1<br><br>; Center of mass control<br>
nstcomm = 1<br><br>; Periodic boundary conditions <br>pbc = xyz<br><br>; Mode for center of mass motion removal<br>comm-mode = Linear<br><br>; Energy minimizing stuff<br>emtol = 2250<br>
emstep = 0.001<br><br><br>For mdrun using position restraints:<br>---------------------------------------------------<br>title = Protein in POPC<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 5000 ; total 10 ps.<br>nstcomm = 1<br>nstxout = 50<br>nstvout = 1000<br>nstfout = 0<br>
nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>tc-grps = Protein Non-Protein<br>tau_t = 0.1 0.1<br>ref_t = 300 300<br>; Energy monitoring<br>energygrps = Protein Non-Protein<br>
; Pressure coupling is not on<br>Pcoupl = berendsen<br>tau_p = 5.0 5.0<br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>Pcoupl_type = semiisotropic<br>; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>Thanking you,<br><br>Yours sincerely,<br>Pawan<br>