Hi all users. When I change the Temperature in the madp file to try to get different result about DNA model's disassociation , but it is strange that result seems to be the same for different Temperature. Even I change the Temperature by 0K ,the disassociation happened.
I have tried to reduce the force between some bond and non-bond, but the effect is not very good. This is part of my mdp file: ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.0001 nsteps =100000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 0.686 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = User rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the Cut-off or DC of the reaction field epsilon-r = 78 ; Method for doing Van der Waals vdw-type = User ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 Can anyone of you tell me what is the reason for that? Thank you in advance. Yang _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
