[gmx-users] DNA not wrapping around CNT in MD simulation

[Justin A. Lemkul]

majid hasan wrote:
> Yes, ideally I didn't want to, but I read somewhere on mailing list that 
> one shouldn't use define = -DFLEXIBLE while running dynamics. So I 
> thought I will use restrained water...
> 
> I'll move back to -DFLEXIBLE though, if I got a successful mdrun for 
> restrained water.
> 

Constraints and restraints are separate ideas.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

If you *restrain* the water, the molecules won't move.  If you *constrain* 
(i.e., using rigid water and not -DFLEXIBLE, which for MD you shouldn't be 
doing) you fix the geometry of a molecule while still allowing it to actually move.

-Justin

> Thanks,
> Majid
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Fri, April 22, 2011 10:44:45 AM
> *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation
> 
> 
> 
> majid hasan wrote:
>  > I just checked and DNA position should not be restrained because I 
> didn't use define = -DPOSRES in .mdp file. I am going to run it for a 
> longer time now, and use position restraints for water
>  >
> 
> What purpose does restraining the water have?  You'll be trying to 
> observe diffusion of your DNA or CNT through an immobile solvent.
> 
> -Justin
> 
>  > Thank You,
>  > Majid.
>  >
>  > ------------------------------------------------------------------------
>  > *From:* Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>  > *Sent:* Fri, April 22, 2011 1:51:47 AM
>  > *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation
>  >
>  > On 4/22/2011 6:48 PM, Mark Abraham wrote:
>  >> On 4/22/2011 4:54 PM, majid hasan wrote:
>  >>> Dear All,
>  >>>
>  >>> I am doing a MD simulation of dna, and cnt in water. I get a stable 
> simulation in which DNA, and CNT wiggles around there positions, but 
> they don't seem to be attracted towards each other. CNT starts in the 
> middle of the box and just moves a little, and DNA starts at top right 
> corner of the box and remains there throughout the simulation.
>  >>>
>  >>> movie of .trr file is here:
>  >>>
>> >> http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg
>  >>>
>  >>> My .mdp files are placed here (both .mdp files are same except for 
> the value of integrator):
>> >> http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp  (used for EM)
>> >> http://phas.ubc.ca/%7Emajid/Project/md.mdp    (used for MD)
>  >>>
>  >>>
>  >>>
>  >>> I created cnt, and dna using following commands:
>  >>> For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select 
> (Selected amber99sb, and TIP3P water model)
>  >>> For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc  (selected 
> amber99sb)
>  >>> For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o 
> cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o 
> cntdnasol.gro
>  >>> In the dna.top file, amber99sb/ions.itp, and a position restraint 
> file was also included along with tip3p.itp. I mentioned it because I am 
> not sure why would it add ions and position restraints on adding water?
>  >>
>  >> #including molecule .itp files adds nothing to the system - only the 
> potential to have molecule type(s). The system is defined in the 
> [system] directive, and must match the corresponding coordinate file.
>  >>
>  >>> It seems that something is wrong with non-bonded interactions, but 
> I don't understand what?
>  >>
>  >> Why aren't you following a proper equilibration protocol before 
> trying to make observations? You might be using position restraints, 
> have your species too far apart, or simply have not simulated long 
> enough to observe any movement. 200ps is an eye-blink.
>  >
>  > Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is 
> unreasonably short. 100,000 of them is far too short to see anything happen.
>  >
>  > Mark
>  >
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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