Hi,
I want to apply rigid SPC/E water model in lammps by applying shake algorithm. But I am not able to understand the certain part of the following command.
fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
In the above mentioned commend b and a means bond and angle. In case of bond what
do 4 and 19 signify? similarly for angle, what do 3 5 2 signify? Please explain by considering 64
water molecules in my simulation box. please let me know any other command is required for applying rigidity of water molecule
How will i decide max # of iterations in each SHAKE solution?
Thank you,
Shamimul Ahsan
Ph.d Student
Indian Institute of Science
Banglaore
India
All of those questions are answered in the LAMMPS manual.
All of those questions are answered in the LAMMPS manual.
Here is the relevant documentation:
https://lammps.sandia.gov/doc/fix_shake.html
The numbers following -b are bond types (and should match the integer
in the first column of the "Bonds" section of your DATA file).
The numbers following -a are angle types (and should match the integer
in the first column of the "Angles" section of your DATA file).
If it helps, here's is an example of building a system of SPC/E water
molecules here:
http://moltemplate.org/doc/moltemplate_manual.pdf#page=17
and a related example (with Na+, CL- ions) here:
http://moltemplate.org/visual_examples.html
This example uses moltemplate (moltemplate.org), however even if you
are not using moltemplate, you should still be able to follow the
example, because the text within the various "write()" and
"write_once()" statements in the "spce.lt" (or "spce_simple.lt") file
exactly matches the text that would appear in a LAMMPS DATA file or
input SCRIPT file, respectively.
Just replace the variables with the corresponding integers. (For
example, replace "@atom:O" with 1, "@atom:H" with 2, "@bond:OH" with
1, and "@angle:HOH" with 1. These are the integers representing the
atom, bond, and angle types for this molecule.) In this example, the
"spce.lt" file contains "group" and "fix shake" commands you will need
in order to run fix shake correctly (as well as the bonds, charges,
and force field parameters you will need).
Hope this helps.
Andrew