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

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 22 19:44:45 CEST 2011

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


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