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.
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 ; 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