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Re: [lammps-users] (no subject)


From: sanchari bhatt <sanchari789byc@...24...>
Date: Fri, 25 Aug 2017 13:12:11 +0530

thanks for your answers ,but instead of doing that i think in oder to put water in methanol why not i merge two datafiles for that i use the command

read_data      data.lammps

read_data water.dat add append offset 1 1 1 0 0 shift 20.0 20.0 20.0


data.lammps is for  methanol  and water.dat is for my water

the simulation is running but when i am not getting any id for water molecule in the trajectory file no hydrogen no oxygen of water molecule only atoms of methanol are present


why this is happenig??
 below is the picture the atom id get merged with each other




any help appreciated!!


On Fri, Aug 25, 2017 at 2:38 AM, Andrew Jewett <jewett@...1937...> wrote:
There is no limit to the number of bond types (and angle types) you want to constrained in the shake command.  Just make sure the group that the fix is acting on includes both the water and the ionic liquid molecules (eg "all" does this)

Have you tried using something like this?

fix water_shake all shake 0.0001 20 0 b 1 5 6 7 a 1

I could be getting the details wrong.  I'm typing this on my phone.  For more details, see:
http://lammps.sandia.gov/doc/fix_shake.html

Also: You may also want to take a look at the molecule builder tools at
http://lammps.sandia.gov/prepost.html
https://sourceforge.net/projects/moleculardynami
These tools will build a LAMMPS DATA file which allows you to have more control over the placement and composition of the molecules in your system and how they are connected together, as well as the use of several canned force fields.  There are several moltemplate examples, for example that show how to build a box of SPC/E water and add ions and other molecules.


andrew

On Aug 24, 2017 1:36 AM, "sanchari bhatt" <sanchari789byc@...24...> wrote:
hello users!!

i want to add water molecules in ionicliquid i am using molecule command to add water molecule but unable to add fix shake as because

i am using fix shake fix SHAKE all shake 0.0001 20 0 b 5 6 7 for my ionicliquid now unable to use again this fix shake for water molecule
fix water_shake all shake 0.0001 20 0 b 1 a 1 mol H2O


Shake Flags

1 1
2 1
3 1

Shake Atoms

1 1 2 3
2 1 2 3
3 1 2 3

Shake Bond Types

1 1 1 1
2 1 1 1
3 1 1 1



what shall i do to add both this commands...as i needed to add both for my ionicliquid and water.
ERROR: More than one fix shake (../fix_shake.cpp:321)



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