On 22 March 2011 22:46, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Elisabeth wrote: > > >> >> On 22 March 2011 22:31, Justin A. Lemkul <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! 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 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 >
-- 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
