[gmx-users] the temperature effect in the simulation

[Justin A. Lemkul]

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
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> --
> ========================================
> 
> 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
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

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

========================================