Hi Steve,
I am working with polymer cross-linking using lammps …i have two doubts:
1 ) While i visualize the lammps output data in VMD … it shows more bonds than actual system consists of… that to only between hydrogen atoms of -CH3 molecules.Is it problem with visualization or with my system. I mention 52 bonds are there but it showing 54 in out put.All actual bonds are there but some more are included.
2)There is any predetermined way to cross-link via lammps . My system is DGEBA/IPD. for which i have to remove hydrogen atoms of amine group in IPD then adding N molecule to DGEBA. The problem is if other molecule is not within range of cutoff …again i have to saturate the system with hydrogen’s. How can it be done via.Lammps.
Thanks in adavnce.
Comments below.
Steve
Hi Steve,
I am working with polymer cross-linking using lammps ...i have two doubts:
1 ) While i visualize the lammps output data in VMD .. it shows more bonds
than actual system consists of.. that to only between hydrogen atoms of
-CH3 molecules.Is it problem with visualization or with my system. I mention
52 bonds are there but it showing 54 in out put.All actual bonds are there
but some more are included.
This is a VMD question. Maybe someone else can answer.
2)There is any predetermined way to cross-link via lammps . My system is
DGEBA/IPD. for which i have to remove hydrogen atoms of amine group in IPD
then adding N molecule to DGEBA. The problem is if other molecule is not
within range of cutoff ...again i have to saturate the system with
hydrogen's. How can it be done via.Lammps.
By "cross-link" do you mean form bonds dynamically during a simulation?
If so, you can look at fix bond/create, but it is isn't flexible enough for
use with all-atom systems. It would have to be extended for that.
If you mean simply form an initial structure with cross-linking, then
that is a pre-processing question. LAMMPS just takes whatever conformation
you give it as input.
Hi Steve,
I am working with polymer cross-linking using lammps ...i have two doubts:
1 ) While i visualize the lammps output data in VMD .. it shows more bonds
than actual system consists of.. that to only between hydrogen atoms of
-CH3 molecules.Is it problem with visualization or with my system. I mention
52 bonds are there but it showing 54 in out put.All actual bonds are there
but some more are included.
this is more a VMD than a LAMMPS question. what VMD shows
you depends on what information you give it. if you read in a
regular lammps dump, then there is no information about bonding
at all communicated to VMD and VMD will do a heuristics based guess.
as you can see from your visualization, a guess can go wrong,
particularly when very limited information is provided.
the bonding information is only contained in a restart or data file,
the latter of which can be read into VMD using the topotools plugin
and then augmented as needed (e.g. to assign atom names, masses,
charges and more) and saved, e.g., as a .psf file which contains
the topology information and can be read directly by VMD.
axel.