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? Read http://www.gromacs.org/Support/Mailing_Lists
