[gmx-users] the temperature effect in the simulation
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 11 22:38:11 CET 2008
He, Yang wrote:
> Hi Justin,
>
> In my case, my box size is adequate to avoid interaction of periodic images of your DNA .For this point, I think is ok.
>
> In fact, when I run this simulation especially for the low temperature, one atom's(Tb1) behavior is strange .No matter how low the temperature is , it will separate from the other matching pair . The others are normal.
>
It looks like you're working with some sort of coarse-grain model for DNA. If
you're developing new parameters, welcome to the headaches that come with such
derivations! Interaction between whatever Tb1 (thymine base?) and the other
atoms may need to be modified. Are you summing the entire base into one
particle? That's pretty extensive mapping that may not capture all the
H-bonding interactions, but I guess that's up to you to decide.
How about ions? Do you have a neutral solution, or do you have unsatisfied
charges from the backbone? That may affect the dynamics as well.
-Justin
> I list my nb and bon file in the attachments .
>
> Thank you
>
>
> ________________________________________
> From: Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, November 11, 2008 1:07 PM
> To: He, Yang; Gromacs Users' List
> Subject: Re: [gmx-users] the temperature effect in the simulation
>
> He, Yang wrote:
>> Hi Justin,
>>
>> My box size is 3.13690 3.73000 2.70000 and I use the user-defined potential functions.
>>
>
> Is that box size adequate to avoid interaction of periodic images of your DNA?
> Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet
> you're getting artefactual PBC interactions.
>
>> #define _FF_GROMACS
>> #define _FF_GROMACS1
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 1 no 1.0 1.0
>>
>> #include "ffyxhnb.itp"
>> #include "ffyxhbon.itp"
>>
>
> Well, if you're defining your own potential, I'd look there for spurious
> repulsive terms. If the DNA is shearing apart, your repulsion between atoms may
> be too large. Combine that with artefactual PBC interactions, and that may give
> rise to your strange behavior.
>
>> This is my ffyxh.itp file
>>
>> Also I have change the value of tau_t by 0.1 but it did not work.
>>
>> Please let me know if you need any further information.
>
> The entirety of the .mdp file, and what you've defined in your *nb.itp *bon.itp
> files, in case there's anything obviously wrong.
>
> -Justin
>
>> Thank you.
>>
>> Yang
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>> Sent: Tuesday, November 11, 2008 12:12 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] the temperature effect in the simulation
>>
>> He, Yang wrote:
>>> Hi all users,
>>>
>>> When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file ,
>>>
>>> ; 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 = 0.001
>>> ref_t = 300
>> I don't know if this is relevant or not, but a coupling constant of 0.001 is
>> exceptionally short. What is the timestep in your simulation? Typically one
>> sees tau_t = 0.1 with a timestep of 0.001-0.002 ps.
>>
>>> ; 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
>>>
>>> It will also disassociate .It is strange.
>> So the dissociation occurs at 0K and 300K? Sounds like something is
>> fundamentally flawed with your system setup. How large is your box? What force
>> field are you using?
>>
>> -Justin
>>
>>> Can anyone of you tell me what is the reason for that?
>>>
>>> Thank you in advance.
>>>
>>> Yang
>>> _______________________________________________
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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