Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero.
Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å? Can anybody help me? Here is my m.mdp file +++++++++++++++++++++++++++++++++++++++++++++++++++++++ title = AB2130 cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1500000 ; total 3.0 ns. nstcomm = 1 nstxout = 1000 ; collect data every 2.0 ps nstvout = 1000 ; collect velocity every 2.0 ps nstfout = 0 nstlog = 0 nstenergy = 1000 ; collect energy every 2.0 ps nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 rvdw_switch = 0.9 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 tau_t = 0.1 0.1 tc-grps = Tmp1 Tmp2 ref_t = 300 0 gen_vel = yes gen_temp = 300.0 acc_grps = Tmp2 accelerate = 0.1 0.1 0.1 gen_seed = 173529 freezegrps = Freez freezedim = Y Y Y +++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- ********************************************* J. Srinivasa Rao Post-doctoral Research Associate Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104 Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx **********************************************
-- 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/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/mailing_lists/users.php