[gmx-users] the Temperature in the mdp.file
David Chan
dichan at ucalgary.ca
Tue Nov 11 21:42:44 CET 2008
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: 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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