Oh, It's OK. Thanks Peter. :-) I used the the same .mdp file sent me by you 1 month ago, for the pre-equilibration of POPC in water.
But as others said here, anisotropic pressure coupling might result in major changes in lipid bilayer. I don't know, but it seems it is better to use anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! Anisotropic would be a better option? Now, I'd like to know which one is suggested to be used for the pre-equilibration before insertion of protein? Anisotropic is suggested? Please make me clear here. Thanks for all explanations. Sincerely, Shima ----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Friday, August 17, 2012 8:19 AM Subject: Re: [gmx-users] Protein-POPC bilayer Can't remember why I said that, since it's not what I used. Stupid autocorrect? Sorry! On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote: > 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 | > ================================================================== -- ================================================================== 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? 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