[gmx-users] the Temperature in the mdp.file

[He, Yang]

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: 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.
>
> Yang
>
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--
Regards,
Yang Ye
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