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/~majid/Project/cntdna.mpg
<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/~majid/Project/lbfgs.mdp
<http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp> (used for EM)
http://phas.ubc.ca/~majid/Project/md.mdp
<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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