Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are restrained runs to remove/dampen clashes and prevent crashes but if you are already running a full md simulation then you don't need to redo those steps.
Also, I don't use DispCorr for C36 lipids (some debates about that can be found on the gromacs mailing list in the past). Setting the constraints to hbonds and using a TIPS3P water model can also help get POPC APL closer to experiment, especially if the starting configuration was highly ordered. On 2012-12-07 10:56:33PM -0800, Shima Arasteh wrote: > Hi again, > > I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 > ff also need such a edition? > Also I'd like to know if these mdp file are applicable in any simulation done > with charmm36? > > > > Sincerely, > Shima > > ________________________________ > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com> > Sent: Friday, November 9, 2012 3:49 PM > Subject: Re: [gmx-users] area per lipid > > > > On 11/9/12 1:46 AM, Shima Arasteh wrote: > > > > > > I pick the snapshots every 10ns, because I don't know how much time this > > system needs to be simulated to reach to the proper APL. > > > > What I'm saying is there are far better ways to assess any trends in your > data > rather than taking 4 snapshots along a much larger trajectory. You can > gather a > lot more detail, and very easily. You're saving snapshots every 2 ps, which > means you will have 20000 data points that can be analyzed, rather than just > 4. > > > The md.mdp dile I used here is: > > > > title = Production run for Water-POPC system > > > > ; Parameters describing the details of the NVT simulation protocol > > integrator = md > > dt = 0.002 > > nsteps = 5000000 > > > > ; Parameters controlling output writing > > nstxout = 1000 > > nstvout = 1000 > > nstenergy = 1000 > > nstlog = 1000 > > > > ; Parameters describing neighbors searching and details about interaction > > calculations > > ns_type = grid > > nstlist = 5 > > rlist = 1.2 > > rcoulomb = 1.2 > > rvdw = 1.2 > > pbc = xyz > > > > You're using a plain cutoff for the van der Waals interactions, which is > incorrect for the CHARMM force fields. You need the following: > > vdwtype = switch > rvdw_switch = 0.8 > rvdw = 1.2 > rlistlong = 1.4 > > The other settings are fine. > > -Justin > > > ; Parameters for treating bonded interactions > > continuation = yes > > constraint_algorithm = LINCS > > constraints = all-bonds > > lincs_iter = 1 > > lincs_order = 4 > > > > ; Parameters for treating electrostatic interactions > > coulombtype = PME > > pme_order = 4 > > fourierspacing = 0.16 > > > > ; Temperature coupling parameters > > tcoupl = Nose-Hoover > > tc-grps = POPC SOL > > tau_t = 0.5 0.5 > > ref_t = 300 300 > > > > ; Pressure coupling parameters > > pcoupl = Parrinello-Rahman > > pcoupltype = semiisotropic > > tau_p = 2.0 > > ref_p = 1.0 1.0 > > compressibility = 4.5e-5 4.5e-5 > > > > > > DispCorr = EnerPres > > gen_vel = no > > nstcomm = 1 > > comm_mode = Linear > > comm_grps =POPC SOL > > > > > > > > Sincerely, > > Shima > > > > > > ________________________________ > > From: Justin Lemkul <jalem...@vt.edu> > > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for > > GROMACS users <gmx-users@gromacs.org> > > Sent: Friday, November 9, 2012 12:20 AM > > Subject: Re: [gmx-users] area per lipid > > > > > > > > On 11/8/12 4:39 AM, Shima Arasteh wrote: > >> Hi, > >> > >> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In > >> order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup > >> as mentioned in articles ), I let the system to be simulated for 40 > >> seconds. To do so, I checked the area per lipid every 10 ns. The results > >> of area per lipid in each step are as below: > >> > >> 1. > >> Top leaflet: 60.44 > >> > >> Bottom leaflet: 59.43 > >> > >> > >> 2. > >> Top leaflet: 61.135 > >> Bottom leaflet: 60.11 > >> > >> 3. > >> Top leaflet: 61.40 > >> > >> Bottom leaflet: 60.38 > >> > >> 4. > >> Top leaflet: 60.27 > >> > >> Bottom leaflet: 59.27 > >> > >> I expected it to approaches the expected amount steadily, but why did I > >> get such a result? How can I get to the appropriate area per lipid? > >> > >> Would you please give me suggestions? Any suggestions would be appreciated. > >> > > > > Without seeing a complete .mdp file, it's hard to say. Why are you picking > > snapshots every 10 ns? You can easily plot APL over time for the entire > > trajectory using the box vectors stored in the .edr file from (Box-X * > > Box-Y)/(number of lipids). You would have to write your own script to do > > the > > calculation, but it's quite straightforward. > > > > -Justin > > > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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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