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

majid hasan pu_majidhasan at yahoo.com
Fri Apr 22 19:01:16 CEST 2011

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

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             
>>movie of .trr file is here:
>>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 
>>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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110422/a378b66c/attachment.html>

More information about the gromacs.org_gmx-users mailing list