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

Mark Abraham Mark.Abraham at anu.edu.au
Sat Apr 23 02:45:22 CEST 2011 

On 4/23/2011 9:21 AM, 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.
>
> Movie of output is here:
> http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg 
> <http://phas.ubc.ca/%7Emajid/Project/msteps/cntdna2000ps.mpg>
> and input em.mdp, and md.mdp files are here:
> EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp 
> <http://phas.ubc.ca/%7Emajid/Project/msteps/lbfgs.mdp>
> MD: http://phas.ubc.ca/~majid/Project/msteps/md.mdp 
> <http://phas.ubc.ca/%7Emajid/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.

You're still not following a sound equilibration protocol. The 
velocities you generate at the start are only roughly correct, and your 
density is probably a bit off. Check out some tutorials, and published 
work on similar systems.

You also need to consider how far apart these species are. If the 
driving force is electrostatic, the forces drop off as 1/r^2, so you can 
wait a long time for those to act over a few nanometers, while 
re-organizing the solvent between them.

In real biochemical systems, one doesn't normally observe a single pair 
of interacting species mate up smoothly. There's a whole pile of things 
that have to happen, and each successful binding probably results from 
very many failed attempts. Having many such pairs over longer periods of 
times means that statistically the events do happen, but that's no good 
to you if you can only simulate a single pair in a short period.

Mark

> 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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