[gmx-users] diffusivity computations
Hi all, I have been trying to estimate the diffusivity of an alanine molecule in water with the .mdp file (for md simualtions) given below. When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreover, the estimated diffusivity (using the g_msd command) looks reasonable (1e-5 cm^2/s) for runs shorter than 0.1 ns. If I run it further, the diffusivity keeps increasing to values of 1e-3 cm^2/s (for 10 ns runs). Any comments or sugestions? ; Preprocessing title = Alanine with Water cpp = /lib/cpp include = define = ; Run Control integrator = md tinit = 0.000 dt = 0.002 nsteps = 25 init_step = 0 comm_mode = None nstcomm = 1 comm_grps = ; Langevin Dynamics ; Energy Miimization ; Shell Molecular Dynamics ; Output Control nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstxtcout = 500 xtc_precision = energygrps = System ; Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 ; Electrostatics and VdW coulombtype = PME rcoulomb_switch = 0 rcoulomb= 0.9 vdwtype = shift rvdw_switch = 0 rvdw= 1.4 DispCorr= no table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft= yes ; Temperature Coupling tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 300 ; Pressure Coupling Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Simulated Annealing ; Velocity Generation gen_vel = yes gen_temp= 300 gen_seed= 173529 ; Bonds constraints = none constraint_algorithm = lincs unconstrained_start = no shake_tol = 0.0001 lincs_order = 4 lincs_iter = 4 lincs_warnangle = 30 morse = no ; Energy Group Exclusions ; NMR Refinement ; Free Energy Perturbation ; Non-equilibrium MD ; Electric Fields ; User Defined Thingies ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] dialanine
Hi, I am seeking help in creating the .pdb file for a dialanine molecule using the databank. I have the parameters for a single alanine molecule. how do i go from here. Thanks Debashis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] diffusivity computations
Hi, I have trying to estimate the diffusivity of an alanine molecule in water with the following .mdp file (for md simualtions). ; Preprocessing title = Alanine with Water cpp = /lib/cpp include = define = ; Run Control integrator = md tinit = 0.000 dt = 0.002 nsteps = 25 init_step = 0 comm_mode = None nstcomm = 1 comm_grps = ; Langevin Dynamics ; Energy Miimization ; Shell Molecular Dynamics ; Output Control nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstxtcout = 500 xtc_precision = energygrps = System ; Neighbor Searching nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 ; Electrostatics and VdW coulombtype = PME rcoulomb_switch = 0 rcoulomb= 0.9 vdwtype = shift rvdw_switch = 0 rvdw= 1.4 DispCorr= no table-extension = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft= yes ; Temperature Coupling tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 300 ; Pressure Coupling Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Simulated Annealing ; Velocity Generation gen_vel = yes gen_temp= 300 gen_seed= 173529 ; Bonds constraints = none constraint_algorithm = lincs unconstrained_start = no shake_tol = 0.0001 lincs_order = 4 lincs_iter = 4 lincs_warnangle = 30 morse = no ; Energy Group Exclusions ; NMR Refinement ; Free Energy Perturbation ; Non-equilibrium MD ; Electric Fields ; User Defined Thingies When I plot the mean square displacement, however I do not see a linear variation with time (which is what I expected). Moreover, the estimated diffusivity (using the g_msd command) looks reasonable (1e-5 cm^2/s) for runs shorter than 0.1 ns. If I run it further, the diffusivity keeps increasing to values of 1e-3 cm^2/s (for 10 ns runs). Any comments or sugestions? ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
