Dear Ondrej - I would start with a high pressure simulation (say, P=100 bar) for 200-500 ps. After this run, the system will be compressed to its more realistic liquid density. Then, go back to P=1 bar and re-equilibrate for 100-200 ps.
I guess, if the temperature were higher, the density would converge faster. What is the shear viscosity of octanol, something around 5-10 cP? Regards, Vitaly Chaban -- Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA > 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 -- 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
