[gmx-users] the Temperature in the mdp.file
yang.he at mavs.uta.edu
Tue Nov 11 20:36:58 CET 2008
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.
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Yang Ye [leafyoung at yahoo.com]
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 <yang.he at mavs.uta.edu> 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.
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