[gmx-users] DNA not wrapping around CNT in MD simulation
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,
> *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:
>>> 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
>> 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
-- gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Please don't post (un)subscribe requests to the list. Use the www interface or
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users