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 <[email protected]>
*To:* Gromacs Users' List <[email protected]>
*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 <[email protected] <mailto:[email protected]>>
> *To:* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> *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 <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
> > *To:* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
> > *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
>
> ========================================
> -- gmx-users mailing list [email protected]
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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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