Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp:
integrator = md dt = 0.002 tinit = 0 nsteps = 5125000 ; 10.250 ns nstcomm = 1 comm_mode = Linear ; Output parameters nstxout = 0 ; every 1 ns nstvout = 0 nstfout = 0 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraints = all-bonds ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = anisotropic ; anisotropic pressure coupling tau_p = 10 compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate from water and shortening xy plane ref_p = 1.0 1.0 1.0 0 0 0 ; Pull code pull = constraint ; pull_geometry = distance ; Pull along the vector connecting the two groups. Components can be selected with pull_dim. pull_dim = N N Y ; put potential only to axis z pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 ; one group to pull pull_group0 = OCT ; reference group (can be empty to set it to 0,0,0) pull_group1 = DRG pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s pull_k1 = 2000 ; kJ mol^-1 nm^-2 however when I list pull-x.xvg I obtain: @ s0 legend "0 Z" @ s1 legend "1 dZ" 0.0000 6.06871 -2.81855 0.0200 6.07793 -2.81861 0.0400 6.08787 -2.81856 0.0600 6.08462 -2.81855 0.0800 6.10028 -2.82007 The situation is even more strange when almost the same mdp with DOPC membrane works fine as can be seen in pull-x.xvg: 0.0000 3.72735 -1.60929 0.0200 3.72727 -1.60929 0.0400 3.7272 -1.60929 0.0600 3.72716 -1.60929 0.0800 3.72715 -1.60929 0.1000 3.72717 -1.60929 Differences in the working case in mdp are only this: compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 0 0 0 pull_group0 = DOPC Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3 I wonder where the difference is, as both logs states that Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 6912 atoms, mass 100624.859 Pull group 1: 15 atoms, mass 194.194 Will apply constraint COM pulling in geometry 'distance' between a reference group and 1 group Pull group 0: 9570 atoms, mass 124631.453 Pull group 1: 15 atoms, mass 146.146 Where should I look and repair? Thank you in advance Karel Zdraví skoro zdravý Karel "Krápník" Berka **************************************************************** RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz ****************************************************************
-- 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
