Fix bond create break

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1

Dear LAMMPS Experts,

I have a N length of polymer chain and have a list of i,j pairs which makes bond with given prob. Those extra bonds who have higher probability appear more number of times and those who have lesser prob. appear less number of times in simulation.

I am using this command.
fix c2 all bond/create 1 1 13 0.97 4 prob 0.078652 76647
fix b2 all bond/break 5 4 0.97 prob 0.078652 76718

1, 13 is the atom id and 4 is bond type.

Now from trajectory output i am calculating how many snapshots have that particular bond.

I am expecting that number of snapshots have particular bond will be proportional to given prob 0.078652.

But i see a very large differences.

Do i need to define different probability in fix command or Is there anything in LAMMPS called rate of bond creation and break

where i can tuned the rate to get the desired probability.

Thanks.

Regards

Ankit Agrawal

Research Student in Computational Biology

The Institute of Mathematical Sciences

India

2

First, there is no guarantee that because you specify 2 commands

with a probability for bond breaking and creating that those probabilitiies

will translate into actual rates of breaking and creation. As the doc

pages for the 2 commands specify, there are many other criteria

applied to determine whether a bond is broken or created. Those would

affect the actual rates.

Second, I don’t think you can have 2 (or more) competing fix bond break/create

commans that are attempting to change the same bonds. This has

been discussed on the mail list previously. This is b/c the data structs

internal to the commands don’t recognize or update due to each other.

Tim Sirk (CCd) can comment on whether your particular use case

has this problem or not.

Steve

3

Hi Ankit. Fix bond create will cruise along without knowing that your type 4 bonds are breaking. There are a couple of threads with some suggestions for this type of system.
Hth,
Tim