Thanks Mark for the hints. I am using a pre equilibrated box for both runs. Can you again explain how Can I interpret this from fluctuations from two runs? Below is the resutls from two versions: Thanks!
4.0.7 Statistics over 733801 steps [ 0.0000 thru 1467.6001 ps ], 1 data sets All averages are exact over 733801 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen 203.778 3623.99 3623.98 -0.00203751 -2.99026 Statistics over 483401 steps [ 500.0000 thru 1466.8000 ps ], 1 data sets All averages are exact over 483401 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen 203.129 3612.58 3612.28 0.168686 163.086 ----------------------------------------------------------------------------------------------------------------- 4.5.3 Statistics over 732501 steps [ 1.0000 through 1466.0000 ps ], 1 data sets All statistics are over 73251 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen 2374.49 570 21081.3 -3251.38 (bar nm) Statistics over 384501 steps [ 1000.0000 through 1769.0000 ps ], 1 data sets All statistics are over 38451 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen 2610.25 1000 21109.9 4638.38 (bar nm) Statistics over 483001 steps [ 500.0000 through 1466.0000 ps ], 1 data sets All statistics are over 48301 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen 1645.07 390 20288.3 -174.289 (bar nm) On 22 March 2011 23:56, Mark Abraham <[email protected]> wrote: > > > On 23/03/11, *Elisabeth * <[email protected]> wrote: > > > > On 22 March 2011 22:46, Justin A. Lemkul <[email protected]> wrote: > >> >> >> Elisabeth wrote: >> >> >>> >>> On 22 March 2011 22:31, Justin A. Lemkul <[email protected] <mailto: >>> [email protected]>> wrote: >>> >>> >>> >>> Elisabeth wrote: >>> >>> Hello, >>> I did two simulations on the same system using versions 4.0.7 >>> and 4.5.3. It seems like the unit of surface tension is not the >>> same in these versions because I am getting ~250 KJ/mol an in >>> 4.0.7 and ~ 5000bar nm in 4.5.3?! How KJ/mol can be converted >>> into bar nm? Can anyone help please. >>> >>> >>> Is this from g_energy output? In past versions, everything was >>> printed as "kJ/mol," even quantities that obviously weren't, like >>> temperature, pressure, etc. >>> >>> >>> Yes, so why are the results so different. I am using exactly the same mdp >>> file.! >>> >>> >> Any pressure-related quantity is going to be subject to enormous >> fluctuations. This has been discussed within the last few days. Without >> seeing the .mdp file and a description of the system, it's hard for anyone >> to comment on what the results might mean. >> > > Thanks. I am working on a pure alkane system, in a box of 3X3X3 which is > extended in Z to create liq/air interface. That is 3X3X6 . What could be > reason for such a big difference in results from two version? Thanks alot! > > > > Look at the size of the fluctuations printed by g_energy. If they're > comparable or larger than your differences, then you are not observing a > statistically significant difference. Over just 2ns of a small system, > that's likely to be the case. Damping such fluctuations requires large > simulations or long times or both. > > You are also generating velocities at the start of this run, so probably > you are including spurious measurements on non-equilibrated configurations > in your statistics. If you'd thought to tell us your command lines, I > wouldn't be guessing :-) You can fix this with g_energy -b, but really you > should separate your equilibration from your production run, even if you > don't really need to, so that all your workflows have similar properties. > Then when you come back to repeat some analysis in a month's time, you don't > have to remember to ignore the first 1ns of this simulation... > > Mark > > > integrator = md > dt = 0.002 > nsteps = 1000000 > > nstenergy = 100 > nstxout = 100 > nstlist = 10 > ns_type = grid > coulombtype = PME > vdw-type = Shift > rcoulomb-switch = 0 > rvdw-switch = 0 > rlist = 1.1 > rcoulomb = 1.1 > rvdw = 1.0 > > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > ;optimize_fft = yes > > Tcoupl = v-rescale > tc-grps = System > tau_t = 0.1 > ref_t = 300 > > pbc = xyz > > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > constraints = all-bonds > constraint-algorithm = lincs > > >> >> -Justin >> >> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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