I am doing DPD on a polymeric system connected by harmonic bonds.
a) Using special bonds lj 1.0 1.0 1.0 and
b) Without any special bonds at all.
From what I understood both the above scenarios should be identical as in both cases there will not be any scaling of forces or energy (because prefactor is 1.0). In one case (with special bonds), it was terminating with "Bond atoms 39 40 missing on proc 10 at step 173 " and without special bonds it was running.
Is my understanding correct? If not what am I missing here?
I am using the latest 27-Nov-2013 version. Running on 12-processors.
Attached is the script(comment out special bonds command to get part b) and their corresponding output.
Data file is generated by chain.py with num of chains = 100 and mon per chain = 64.
I am doing DPD on a polymeric system connected by harmonic bonds.
a) Using special bonds lj 1.0 1.0 1.0 and
b) Without any special bonds at all.
From what I understood both the above scenarios should be identical as in
no, they should not.
both cases there will not be any scaling of forces or energy (because
prefactor is 1.0). In one case (with special bonds), it was terminating with
"Bond atoms 39 40 missing on proc 10 at step 173 " and without special bonds
it was running.
Is my understanding correct? If not what am I missing here?
you are wrong. the default setting for special_bonds is lj/coul 0.0 0.0 1.0
I used special_bonds lj 1.0 1.0 1.0 because I wanted DPD interactions to be
present between every particle irrespective of whether they are bonded or
not.
I did simulations with and without special_bonds as a check.
Side note: special_bonds lj 0.0 0.0 1.0 will nullify the 1-2 and 1-3 pair
interactions, wont they, which is not I wanted.
you will get different behavior with 2 different
settings. If you are losing atoms it typically
means they are interacting too strongly and one
is getting blown out of the simulation box.
Sorry for the confusion in my lines. Thanks for the replies. Couple of more questions
Q1: In the first mail when Axel comment “it should not”, are you referring to it should not be “equal” or it should not “matter”? I am sorry that I did not understand this. I dont see any reason why they should not be the same if i have the same input configs (apart from the differences that come from stochastisity)
Q2: Even if i override the default values of special_bonds lj/coul, it should work, shouldn’t it? So if i use 0.0 1.0 1.0, it means there will not any DPD interactions between the paired molecules or will it still stay in default?
Q3: Any ideas as to what should be the general communicate cutoff for DPD simulations (i know that this depends on the system size and parameters chosen). But a value of communicate cutoff 2.0 is blowing up where as a value of 4.0 is not. I am not sure whether it is a large value.
Sorry for the confusion in my lines. Thanks for the replies. Couple of more
questions
Q1: In the first mail when Axel comment "it should not", are you referring
to it should not be "equal" or it should not "matter"? I am sorry that I did
it should not be equal.
not understand this. I dont see any reason why they should not be the same
i do see a good reason.
if i have the same input configs (apart from the differences that come from
stochastisity)
i already explained. the default settings for special_bonds are
lj/coul 0.0 0.0 1.0 which will be applied if you omit the
special_bonds command. *many* commands in LAMMPS that modify *global*
settings have defaults that will be used, if you omit that command.
Q2: Even if i override the default values of special_bonds lj/coul, it
should work, shouldn't it? So if i use 0.0 1.0 1.0, it means there will not
"it should work" is a horribly imprecise statement. nobody knows what
you are referring to exactly. only if you ask precise questions, you
can expect specific answers.
any DPD interactions between the paired molecules or will it still stay in
default?
there is a global setting for exclusions (well, one for lj and one for
coulomb) and the special_bonds command adjusts it.
thus i don't understand what you mean by your statement.
Q3: Any ideas as to what should be the general communicate cutoff for DPD
simulations (i know that this depends on the system size and parameters
chosen). But a value of communicate cutoff 2.0 is blowing up where as a
value of 4.0 is not. I am not sure whether it is a large value.
there is no need to set the communicate cutoff unless your bonds may
be stretched longer than the largest cutoff plus skin.
please re-read the documentation for the communicate command. it
explains what the cutoff does and how it is applied.
