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

majid hasan pu_majidhasan at yahoo.com
Fri Apr 22 19:56:35 CEST 2011

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 


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.


> 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 
>>> 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 
>>> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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