The pressure on a (real-life) membrane is not isotropic, edges are under tension. so using the p-couple “surface-tension” - with water layers is appropriate.
If you use p-couple = isotropic you should end up with a micelle because the hydrophobic effects are significant. p > On Jun 14, 2019, at 11:18 PM, Prasanth G, Research Scholar > <prasanthgha...@sssihl.edu.in> wrote: > > Dear Bratin, > > When I am using a semiisotropic condition the pbc box is > deforming/compressing pushing the lipid bilayer apart. I am attaching the > screenshots of the system at the beginning(normal.png) of production run as > well as at the end of 30ns simulation (elongated.png) for your reference. > > This was my production mdp (md.mdp) file: > ---- > title = pro-DPP-LIG Production MD > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 15000000 ; 2 * 15000000 = 30000 ps (1 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 1000 ; save coordinates every 2 ps > nstvout = 1000 ; save velocities every 2 ps > nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps > nstenergy = 1000 ; save energies every 2 ps > nstlog = 1000 ; update log file every 2 ps > ; Bond parameters > continuation = yes ; Restarting after NPT > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.2 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) > rvdw = 1.2 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = Nose-Hoover ; More accurate thermostat > tc-grps = Protein_LIG_DPP Water_and_ions ; > tau_t = 0.5 0.5 ; time constant, in ps > ref_t = 323 323 ; reference temperature, one > for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, > independent z > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) > compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no ; Velocity generation is off > ; COM motion removal > ; These options remove motion of the protein/bilayer relative to the > solvent/ions > nstcomm = 1 > comm-mode = Linear > comm-grps = Protein_LIG_DPP Water_and_ions > --- > *LIG is ligand and > DPP is DPPC. > > Thank you. > > normal.png > <https://drive.google.com/a/sssihl.edu.in/file/d/1BLR5UG8jwWnwnS4wmt1W-qIks4YCijPp/view?usp=drive_web> > > elongated.png > <https://drive.google.com/a/sssihl.edu.in/file/d/14yDNhlBJKbhhgFdpIYtr7SGhQIMoJrq6/view?usp=drive_web> > > On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar < > prasanthgha...@sssihl.edu.in> wrote: > >> Dear all, >> >> Can someone please tell me if it is okay to use isotropic pcoupltype for a >> membrane protein simulation? Are there any disadvantages? >> >> Also, why is semiisotropic preferred over isotropic, in membrane protein >> simulations.. >> >> Thank you. >> -- >> Regards, >> Prasanth. >> > > > -- > Regards, > Prasanth. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.