You have to do some energy minimization before you run mechanical properties

http://www.jocpr.com/articles/molecular-dynamic-simulation-of-the-mechanical-properties-of-pisio2-nanocomposite-based-on-materials-studio.pdf

Simulation Process of Mechanical Properties on Mate

rials Studio

The steps of model construction and calculation pro

cess of molecular dynamics are as follows:

1. To build the crystal model of nanoparticle

Import the model from the material database, select

File| Import | Examples |Documents |3D Modelfrom t

he menu

bar to get the model required.Then select Build| Bu

ild Nanostructure| Nanoclusterfrom the menu bar

，

set the shape

and particle size, click Build button and the nanoc

luster required model is obtained.

2.To build the polymer chain

Sketch a fragment or open a 3D atomistic document c

ontaining one., set Head Atom and Tail Atom from th

e menu

bar as Build | Build Polymers | Repeat Unit to get

the repeated unit , select Build | Build Polymers |

Homopolymer to

set the chain length and the tacticity, obtain the

model of the polymer chain.

3.Geometry Optimization

In molecular dynamics simulation, the structure whi

ch is not optimized will obtain erroneous results i

n the

subsequent simulation. Select Modules| Forcite| Cal

culation to open the Calculation dialog, Geometry O

ptimization

is selected in the Task dropdown list to optimize t

he initial cell model so as to obtain the stable lo

w-energy structure

cell. The Smart algorithm is usually chosen for the

simulation, and the simulation time should be adju

sted to the size

of the structure.The results of the geometry optimi

zation include the files of the density curve, ener

gy, convergence,

cell size diagram and the results file.

4.To build the nanocomposite unit cell model

The Amorphous Cell module is used to construct the

periodic structure model of complex amorphous mater

ials.

Select Build | Build Crystal to open the Build Crys

tal dialog, set the size to get a periodic empty ce

ll model, then

copy and paste the particle cell model to this empt

y cell, make the body centroid of the cell coincide

with the body

centroid of the nanoparticle, set the fractional co

ordinates of the particle centroid as (0.5,0.5,0.5)

. When the cell

model of nanocomposite is build, select Modules| Am

orphous Cell| Calculation to open the Calculation d

ialog,

Packing option is chosen in Task dropdown list, the

COMPASS option is selected from the force field ta

b, set the

relevant parameters, and “pack in isosurface enclos

ed volume” is selected, the encapsulation of nanopa

rticles and

polymer can be done. The files of Calculation resul

ts will display the detailed information of each pa

rameter set,

such as the number of themolecular chains packaged

into the cell and the final energy value of the cel

l model of

composites

5.Calculation of Molecular Dynamics

To obtain the true density of material, the Molecul

ar Dynamics Simulation is necessary. The cell densi

ty gradually

increases under external pressure, and the system c

an be further compressed by increasing the pressure

via NPT

simulation. Select Modules| Forcite| Calculation to

open the Dynamics dialog. The NPT option is select

ed from the

More tab. Generally, the NPT simulation is more tha

n once, but the appropriate densityalso can be obta

ined by

increasing the pressure via NPT simulation just for

once.

6.Mechanical Properties Simulation

Select Modules| Forcite| Calculation to open the Me

chanical Properties dialog. Generally the last 10 f

rames of the

stable structures are calculated. The appropriate p

recision is set and other parameters are kept the d

efault

values.The relevant information of the initial para

meters, the stiffness matrix and flexibility matrix

of thecomposite,

bulk modulus and shear modulus which are calculated

via Reuss

，

Voigt and Hill formula respectively, the stress

along X ,Y and Z direction which aresetby initial p

arameters and Lame constants are obtained from the

Calculation

results files.

I am facing some issue and I am new in simulation. I want to prepare a membrane using PDMS polymer along with certain percentage of ZIF-8 in it. For this I need only some part of ZIF-8 not the entire unit cell and for this I have to select some of the part but when I take out some of it part I am not able optimize its geomatery using compass I face the forcefield error . And if i use universal forcefield then when I make the membrane with pdms polymer the bonds lengths and angles of ZIF-8 changes and it becomes totally disorder. Please help me out if you have understand what problem I am facing. Waiting for your positive response

Monika Warzecha Mam, I am working on the same concept i.e. calculation of mechanical properties using materials studio for pharmaceutical excipients. Even I was stuck in the same step but after the equilibration and dynamics runs I got some agreeable results.

As it's been a long time you have posted this query, if its possible can you suggest some way out for my problem-

How to calculate stress value using the compliance matrix which we get after mechanical property calculation using the constant strain approach. I need to plot a stress-strain curve plot using FORCITE module. Also, I don't have access to CASTEP so FORCITE module is the only option left.

Mohamed Arar Sir, it will be great if you suggest me a way out for the same.

Thank you,

Sanjali Panigrahi

M.S. (Pharmaceutics)

NIPER Mohali, India

Sanjali Panigrahi You will see the corresponded stress-strain matrix during the running process. The issue is, the data will appear and will be discarded. So you need to mannually wait for the result to come out and make a copy