Thanks for your help. :) On 23 March 2011 07:47, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Mark Abraham wrote: > >> On 23/03/2011 3:39 PM, Elisabeth wrote: >> >>> 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! >>> >> >> IIRC the contents of the .edr file didn't change across these versions, >> but the reporting of computed quantities did, so I'd make my life simpler >> and use only the 4.5.3 g_energy. >> >> > Actually, 4.5.3 may have the bug: > > http://redmine.gromacs.org/issues/696 > > The quantities in the .edr file are correct, but the output from g_energy > is nonsense. It was fixed for 4.5.4. > > -Justin > > Both simulations have a much higher value for the root-mean-squared >> deviation from the average (i.e. standard deviation) than for the average. >> So that means your data set looks something like "10000 20 6543 200 23444 >> 23434 15 500 3444". Look at the .xvg file that is produced. You need a heck >> of a lot of such data to have confidence that your sample average reflects >> the true average. If you haven't got that pile of data, then you haven't >> observed the average with any confidence. This is normal for quantities >> computed from fluctuations in atomic positions. They're macroscopic >> quantities, and have to be observed over a lot of microscopic >> configurations. >> >> Be sure to check visually that your system is doing what you hope it is >> doing. >> >> Mark >> >> >>> 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 <mark.abra...@anu.edu.au <mailto: >>> mark.abra...@anu.edu.au>> wrote: >>> >>> >>> >>> On 23/03/11, *Elisabeth * <katesed...@gmail.com >>> <mailto:katesed...@gmail.com>> wrote: >>> >>>> >>>> >>>> On 22 March 2011 22:46, Justin A. Lemkul <jalem...@vt.edu >>>> <mailto:jalem...@vt.edu>> wrote: >>>> >>>> >>>> >>>> Elisabeth wrote: >>>> >>>> >>>> >>>> On 22 March 2011 22:31, Justin A. Lemkul <jalem...@vt.edu >>>> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >>>> >>>> <mailto:jalem...@vt.edu>>> 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 <http://vt.edu> | (540) 231-9080 >>>> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> ======================================== >>>> -- gmx-users mailing list gmx-users@gromacs.org >>>> <mailto: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 >>>> <mailto:gmx-users-requ...@gromacs.org>. >>>> >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto: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 >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >> > -- > ======================================== > > 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 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 >
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