<p>Dear Gmx users,</p>
<p>I am working on a transmembrane protein and my system contains protein, DPPC<br>bilayer, water (spc) and ions. After preparing my system for simulation I<br>have successfully performed the energy minimization, I am facing a problem<br>
at the nvt equilibration phase of 100ps, the lipid molecules enter the voids<br>in the solvent leaving the protein naked. I have already used position<br>restraint at the inflate.gro steps, now I have read that I can use the<br>
option to freeze the groups which I can do at the z axis to avoid the lipid<br>headgroups to enter the void of the solvent. The manual suggests starting<br>with freezing in a constant volume simulation and afterwards using position<br>
restraints in conjunction with constant pressure.</p>
<p>Now, Is it feasible if I freeze the lipids in z-axis for the whole course of<br>simulation or should I do it only during the equilibration phase?</p>
<p>Is there any alternative which I can use during simulation to avoid this?</p>
<p>My nvt.mdp is:</p>
<p>-----------------------------------------------------------</p>
<p>title = NVT equilibration for B3-DPPC</p>
<p>define = -DPOSRES ; position restrain the<br>protein</p>
<p>; Run parameters</p>
<p>integrator = md ; leap-frog integrator</p>
<p>nsteps = 50000 ; 2 * 50000 = 100 ps</p>
<p>dt = 0.002 ; 2<br>fs</p>
<p>; Output control</p>
<p>nstxout = 100 ; save coordinates<br>every 0.2 ps</p>
<p>nstvout = 100 ; save velocities every<br>0.2 ps</p>
<p>nstenergy = 100 ; save energies every 0.2<br>ps</p>
<p>nstlog = 100 ; update log file<br>every 0.2 ps</p>
<p>; Bond parameters</p>
<p>continuation = no ; first dynamics run</p>
<p>constraint_algorithm = lincs ; holonomic constraints</p>
<p>constraints = all-bonds ; all bonds (even<br>heavy atom-H bonds) constrained</p>
<p>lincs_iter = 1 ;<br>accuracy of LINCS</p>
<p>lincs_order = 4 ; also<br>related to accuracy</p>
<p>; Neighborsearching</p>
<p>ns_type = grid ; search neighboring<br>grid cels</p>
<p>nstlist = 5 ; 10 fs</p>
<p>rlist = 1.2 ; short-range<br>neighborlist cutoff (in nm)</p>
<p>rcoulomb = 1.2 ; short-range<br>electrostatic cutoff (in nm)</p>
<p>rvdw = 1.2 ; short-range van<br>der Waals cutoff (in nm)</p>
<p>; Electrostatics</p>
<p>coulombtype = PME ; Particle Mesh Ewald for<br>long-range electrostatics</p>
<p>pme_order = 4 ; cubic<br>interpolation</p>
<p>fourierspacing = 0.16 ; grid spacing for FFT</p>
<p>; Temperature coupling is on</p>
<p>tcoupl = V-rescale ; modified<br>Berendsen thermostat</p>
<p>tc-grps = Protein DPPC SOL_CL- ; three coupling groups -<br>more accurate</p>
<p>tau_t = 0.1 0.1 0.1<br>; time constant, in ps</p>
<p>ref_t = 323 323 323 ;<br>reference temperature, one for each group, in K</p>
<p>; Pressure coupling is off</p>
<p>pcoupl = no ; no pressure coupling<br>in NVT</p>
<p>; Periodic boundary conditions</p>
<p>pbc = xyz ; 3-D PBC</p>
<p>; Dispersion correction</p>
<p>DispCorr = EnerPres ; account for cut-off vdW<br>scheme</p>
<p>; Velocity generation</p>
<p>gen_vel = yes ; assign velocities from<br>Maxwell distribution</p>
<p>gen_temp = 323 ; temperature for Maxwell<br>distribution</p>
<p>gen_seed = -1 ; generate a random seed</p>
<p>; COM motion removal</p>
<p>; These options remove motion of the protein/bilayer relative to the<br>solvent/ions</p>
<p>nstcomm = 1</p>
<p>comm-mode = Linear</p>
<p>comm-grps = Protein_DPPC SOL_CL-</p>
<p>----------------------------------------------------------------------------------------<br>thanks,<br>Parul Tewatia</p>