Hi Yang Ye, Thank you for your reply. When I change the temperature, the disassociation about the two strands of DNA always happened even though the temperature is reduced to 0K. It is absolutely impossible.
I think it is a real disassociation. So I am confused about the phenomenon . Any further suggestions ? I really appreciate your help. Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Yang Ye [EMAIL PROTECTED] Sent: Monday, November 10, 2008 6:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the Temperature in the mdp.file Is it a real diassociation or an illusion? Visualize with PBC in mind. To put them back, use trjconv to center one chain of the DNA and output the two chains. On 11/11/08, He, Yang <[EMAIL PROTECTED]> wrote: 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 > -- Regards, Yang Ye _______________________________________________ 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 _______________________________________________ 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
