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

majid hasan pu_majidhasan at yahoo.com
Sat Apr 23 01:21:32 CEST 2011 

Okay, thanks, I removed restraints from water.

 In the final simulation, I increased the simulation time from 20ps to 2000ps to 
see if they wrap around. However in .trr output, CNT and DNA remain stable, 
jiggles around and jump across the box in a weird manner (might have something 
to do with periodic boundary conditions?) but don't seem to be attracted towards 
each other. 

Movie of output is here:
http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg
and input em.mdp, and md.mdp files are here:
EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp
MD: http://phas.ubc.ca/~majid/Project/msteps/md.mdp

Commands that I have been using to build input coordinates, and topologies are 
below:

 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 :        genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 
20 

For solvation:     genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro

I have no clue what is wrong with the simulation, and any help is much 
appreciated. 

Thanks,
Majid


________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Fri, April 22, 2011 10:59:22 AM
Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation



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

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