Hi He Yang,
I've never worked with DNA simulations before, but I don't think you
should have a timestep of 0.0001 ps. For proteins, people commonly use
0.002ps, i.e 20 x larger than what you are using. The number of steps
you are using is quite small too. Also, where did you get your rlist =
0.686 value? I've never seen this before (which may just be me), but it
may be good to have another mdp file as a reference (see tutorials or
mailing list?). An online tutorial may also give you an indication of
what kind of dissociating/movement to expect, which may help you
evaluate what you're observing in your simulations.
D.
He, Yang wrote:
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
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--
Regards,
Yang Ye
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