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

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 23 02:18:50 CEST 2011 


majid hasan wrote:
> 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. 
> 

2 ns is still what would be considered an extremely short simulation. 
Large-scale behavior may take tens or hundreds of ns.  I have no experience with 
DNA-CNT interactions, but for protein-protein interactions (even for small 
peptides), such time scales are certainly necessary.

> Movie of output is here:
> http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg

I don't see anything odd about this at all.  If you're having periodicity 
issues, trjconv is the tool to take care of that.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

> and input em.mdp, and md.mdp files are here:
> EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp
> <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
> 
> <http://phas.ubc.ca/~majid/Project/msteps/md.mdp>I have no clue what is 
> wrong with the simulation, and any help is much appreciated. 
> 

Likely nothing is "wrong," you just aren't simulating long enough.

-Justin

> 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 <mailto:jalemkul at vt.edu>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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> <mailto: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> <mailto: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> <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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-- 
========================================

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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