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

[Justin A. Lemkul]

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>
> *To:* Discussion list for GROMACS users <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
> 

-- 
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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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