Hi GMX users! I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. But I always got something completely different. Some cluster of the molecules at the bottom of the simulation box, far away from dense cube configuration. You can see picture here: https://picasaweb.google.com/okroutil/Science#5738216101659210130. I tried different thermo- and barostats, different coupling times, compressibility, first NVT then NPT equil., but with no success. I also tried more "chaotic" initial configuration generated with genbox -ci ...gro - nmol 125 -box 5 5 5, no success. So my question is: is there some simulation protocol or some setting (higher pressure at the beginning of equilibration?), any trick suitable for this type of solvent? Till now I worked only with water and surfaces, so this is new area for me...
Thank you very much for any answer and have a nice day! Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian University, Czech Republic) P.S.: I used gaff ff and topologies downloaded from http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT eq. input: integrator = md dt = 0.002 nsteps = 500000 comm_mode = linear nstcomm = 1000 nstxout = 0 nstxtcout = 100 nstvout = 0 nstfout = 0 nstlog = 500 nstlist = 10 ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 constraints = none constraint_algorithm = lincs ;shake_tol = 0.00001 lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft = yes ; Nose-Hoover temperature coupling Tcoupl = berendsen tau_t = 1 tc_grps = system ref_t = 298. ; No Pressure Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.6e-5 ref_p = 1.0 ; OTHER periodic_molecules = no pbc = xyz gen_vel = yes gen_temp = 298.15 gen_seed = -1-- Ondřej Kroutil ,, Faculty of Health and Social Studies ----"))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: [email protected] >------ O Mobile: +420 736 537 190 -- 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
