<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><a href="mailto:gmx-users@gromacs.org"><font size="3" face="Times New Roman">gmx-users@gromacs.org</font></a></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3" face="Times New Roman">Dear Gmx users,</font></p>
<p style="MARGIN: 0in 0in 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman">I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of 100ps, the lipid molecules enter the voids in the solvent leaving the protein naked. I have already used position restraint at the inflate.gro steps, now I have read that I can use the option to freeze the groups which I can do at the z axis to avoid the lipid headgroups to enter the void of the solvent. </font></font><font size="3" face="Times New Roman"> The manual suggests starting with freezing in a constant volume simulation and afterwards using position restraints in conjunction with constant pressure. </font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><font size="3" face="Times New Roman">Now, Is it feasible if I freeze the lipids in z-axis for the whole course of simulation or should I do it only during the equilibration phase?</font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><font size="3" face="Times New Roman">Is there any alternative which I can use during simulation to avoid this?</font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><font size="3" face="Times New Roman">My nvt.mdp is:</font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><font size="3" face="Times New Roman">-----------------------------------------------------------</font></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">title<span style="mso-tab-count: 2"> </span>= NVT equilibration for B3-DPPC </font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">define<span style="mso-tab-count: 2"> </span>= -DPOSRES<span style="mso-tab-count: 1"> </span>; position restrain the protein</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Run parameters</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">integrator<span style="mso-tab-count: 1"> </span>= md<span style="mso-tab-count: 2"> </span>; leap-frog integrator</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nsteps<span style="mso-tab-count: 2"> </span>= 50000<span style="mso-tab-count: 2"> </span>; 2 * 50000 = 100 ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">dt<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>= 0.002<span style="mso-tab-count: 2"> </span>; 2 fs</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Output control</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstxout<span style="mso-tab-count: 2"> </span>= 100<span style="mso-tab-count: 2"> </span>; save coordinates every 0.2 ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstvout<span style="mso-tab-count: 2"> </span>= 100<span style="mso-tab-count: 2"> </span>; save velocities every 0.2 ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstenergy<span style="mso-tab-count: 1"> </span>= 100<span style="mso-tab-count: 2"> </span>; save energies every 0.2 ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstlog<span style="mso-tab-count: 2"> </span>= 100<span style="mso-tab-count: 2"> </span>; update log file every 0.2 ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Bond parameters</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">continuation<span style="mso-tab-count: 1"> </span>= no<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>; first dynamics run</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">constraint_algorithm = lincs<span style="mso-tab-count: 1"> </span>; holonomic constraints </font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">constraints<span style="mso-tab-count: 1"> </span>= all-bonds<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>; all bonds (even heavy atom-H bonds) constrained</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">lincs_iter<span style="mso-tab-count: 1"> </span>= 1<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>; accuracy of LINCS</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">lincs_order<span style="mso-tab-count: 1"> </span>= 4<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>; also related to accuracy</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Neighborsearching</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">ns_type<span style="mso-tab-count: 2"> </span>= grid<span style="mso-tab-count: 2"> </span>; search neighboring grid cels</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstlist<span style="mso-tab-count: 2"> </span>= 5<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>; 10 fs</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">rlist<span style="mso-tab-count: 2"> </span>= 1.2<span style="mso-tab-count: 2"> </span>; short-range neighborlist cutoff (in nm)</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">rcoulomb<span style="mso-tab-count: 1"> </span>= 1.2<span style="mso-tab-count: 2"> </span>; short-range electrostatic cutoff (in nm)</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">rvdw<span style="mso-tab-count: 2"> </span>= 1.2<span style="mso-tab-count: 2"> </span>; short-range van der Waals cutoff (in nm)</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Electrostatics</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">coulombtype<span style="mso-tab-count: 1"> </span>= PME<span style="mso-tab-count: 2"> </span>; Particle Mesh Ewald for long-range electrostatics</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">pme_order<span style="mso-tab-count: 1"> </span>= 4<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>; cubic interpolation</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">fourierspacing<span style="mso-tab-count: 1"> </span>= 0.16<span style="mso-tab-count: 2"> </span>; grid spacing for FFT</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Temperature coupling is on</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">tcoupl<span style="mso-tab-count: 2"> </span>= V-rescale<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>; modified Berendsen thermostat</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">tc-grps<span style="mso-tab-count: 2"> </span>= Protein DPPC SOL_CL-<span style="mso-tab-count: 1"> </span>; three coupling groups - more accurate</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">tau_t<span style="mso-tab-count: 2"> </span>= 0.1<span style="mso-tab-count: 1"> </span>0.1<span style="mso-tab-count: 1"> </span>0.1<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>; time constant, in ps</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">ref_t<span style="mso-tab-count: 2"> </span>= 323 <span style="mso-tab-count: 1"> </span>323<span style="mso-tab-count: 1"> </span>323<span style="mso-tab-count: 1"> </span><span style="mso-spacerun: yes"> </span>; reference temperature, one for each group, in K</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Pressure coupling is off</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">pcoupl<span style="mso-tab-count: 2"> </span>= no <span style="mso-tab-count: 2"> </span>; no pressure coupling in NVT</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Periodic boundary conditions</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">pbc<span style="mso-tab-count: 2"> </span><span style="mso-spacerun: yes"> </span>= xyz<span style="mso-tab-count: 2"> </span>; 3-D PBC</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Dispersion correction</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">DispCorr<span style="mso-tab-count: 1"> </span>= EnerPres<span style="mso-tab-count: 1"> </span>; account for cut-off vdW scheme</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; Velocity generation</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">gen_vel<span style="mso-tab-count: 2"> </span>= yes<span style="mso-tab-count: 2"> </span>; assign velocities from Maxwell distribution</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">gen_temp<span style="mso-tab-count: 1"> </span>= 323<span style="mso-tab-count: 2"> </span>; temperature for Maxwell distribution</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">gen_seed<span style="mso-tab-count: 1"> </span>= -1<span style="mso-tab-count: 2"> </span>; generate a random seed</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; COM motion removal</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">; These options remove motion of the protein/bilayer relative to the solvent/ions</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">nstcomm<span style="mso-tab-count: 2"> </span>= 1</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">comm-mode<span style="mso-tab-count: 1"> </span>= Linear</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">comm-grps<span style="mso-tab-count: 1"> </span>= Protein_DPPC SOL_CL-</font></span></p>
<p style="MARGIN: 0in 0in 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-SIZE: 10pt"><font face="Times New Roman">----------------------------------------------------------------------------------------</font></span></p>
<div>thanks,</div>
<div>Parul Tewatia<br><br></div>