In "2.1.6. Membrane bilayer construction" part of the article you mentioned:
Asingle POPC molecule is parameterized using a CHARMM36 force field conversion for GROMACS7. The result- ing system,which consists of around 238 lipids is then equilibrated for at least 50 ns at 310 K and 1 atm under NPT ensemble with anisotropic pressure coupling or until the are a per lipid converges close to the consensus value of around 63–65Å per headgroup. This is where I asked the question about. Thanks. Sincerely, Shima ----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, August 17, 2012 7:17 AM Subject: Re: [gmx-users] Protein-POPC bilayer Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, in caes you lost it from the time before: You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/ Parinello-Rahman with the paraeters below was stable for me with 238 POPC and 21524 water. integrator = md ; leap-frog integrator nsteps = 2500000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps continuation = yes ; NOT first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-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 cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; 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 ; modified Berendsen thermostat tc-grps = POPC SOL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 300 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = POPC SOL On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote: > You always use semi-isotropic for bilayer work. The Z is decoupled from x-y > due to symmetry. > > I don't think I mention anything differently in the paper. > > Pcoupltype = semiisotropic > > > On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote: > > > > Hi, > > > > I have a question about the Protein-POPC system: > > To insert a protein in lipid bilayer, I am suggested to simulate POPC in > > water separately before insertion, it might decrease the time of final > > simulation. It's OK! > > > > In the article suggested me by dear Peter C. Lai, I read that POPC was > > simulated in anisotropic pressure coupling at first and then after > > insertion of protein, semi-isotropic pressure coupling is applied. > > Now, would you please telling me why you used this procedure? > > And, > > Would my system be correct if I use semi-isotropic pressure coupling > > instead of anisotropic pressure coupling for the first step? > > > > Thanks in advance for your replies. > > > > > > Sincerely, > > Shima > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
