fix rigid

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1

Hi all,

I am modelling DNA as a cylinder (a few atoms at the center) with phosphate on the surface of DNA forming double strands. The DNA is rigid(central atoms + phosphates (2 strands) and I want to let it to rotate around the central axis. I am trying to use “fix rigid” in a very simple system of just 2 DNA (two rigid bodies). 2 DNAs are initially parallel along z axis (separated along x axis). As I ran the code 2 DNA tilts (not parallel any more) although I have turned off x and y component of Torque and all Force components.
I want them to remain parallel to each other and only rotate along z axis. Is there anything that I have not considered?

BTW there is periodic boundary condition in the system and DNA is repeated along the z axis.

I really appreciate any help.

Best,
Shahzad

group rodions1 type 1
group rodions2 type 2
group hrod1 type 3
group hrod2 type 4
group ax type 1 2
group rods type 3 4
group r1 type 1 3
group r2 type 2 4
group r type 1 2 3 4

mass 1 20
mass 2 20
mass 3 20
mass 4 20

#set group rodions1 image NULL NULL 0
#set group rodions2 image NULL NULL 0
#set group hrod1 image NULL NULL 0
#set group hrod1 image NULL NULL 0

pair_style lj/cut/coul/long 10

pair_coeff 1 1 0.0 1.0 # Rodion1-Rodion1
pair_coeff 1 2 0.0 1 # Rodion1-Rodion2
pair_coeff 2 2 0.0 1.0 # Rodion2-Rodion2
pair_coeff 1 3 1.553 9 18 # Rodion1-hrod1
pair_coeff 2 3 0 0 # Rodion2-hrod1
pair_coeff 3 3 0.0 1 # hrod1-hrod1
pair_coeff 1 4 0.0 0 # Rodion1-hrod2
pair_coeff 2 4 1.553 9 18 # Rodion2-hrod2
pair_coeff 3 4 0.0 1.0 # hrod1-hrod2
pair_coeff 4 4 0.0 1.0 # hrod2-hrod2

kspace_style ewald 0.0001

dielectric 72
neighbor 2.0 bin

#fix 3 rodions1 setforce 0.0 0.0 0.0
#fix 4 rodions2 setforce 0.0 0.0 0.0

#fix 1 all rigid group 2 hrod1 hrod2 force * off off off torque * off off on
fix 1 r1 rigid single force 1 off off off torque 1 off off on
fix 2 r2 rigid single force 1 off off off torque 1 off off on

dump 1 hrod1 custom 1000 rod1 id type x y z
dump 2 hrod2 custom 1000 rod2 id type x y z
dump 3 ax custom 1000 ax id type x y z

2

Things like this are difficult to explain only using words.
Can you draw a picture of what you want your model to look like?

In particular, how should each "monomer" of DNA connected to the next
monomer? (Are they connected by the central atoms, or by atoms in the
two backbones?)

Cheers
Andrew

3

Do you initialize velocities? If so, turning
off forces/torques will not affect the initial
velocities.

Steve

4

Hi Steve and Andrew,

Thanks for your replies.

Andrew, phosphates interact with Central atom considering a Lennard-Jones potential and they are fixed at their position as the whole DNA is a single rigid body. I attached a picture of my system.

Steve, I set the velocity of all particles equal to zero, but still the same results. In the attached plot, the configurations of system at two different time are represented.

Best,
Shahzad

pic_DNA.pdf (761 KB)

5

Your original post didn’t say what the problem/question
is that you are asking about. Nor how you are convinced
that something wrong is happening.

Steve