Dear All,
could anyone advise me step-by-step how to calculate mechanical properties in Materials Studio? As an example I've chosen L-cystine and wanted to repeat calculation that have been already done in http://pubs.acs.org/doi/pdf/10.1021/cg501485e
What I'm doing is:
1. import .cif file
2. rebuild crystal
3. Go to Modules->FORCITE->task:mechanical properties->quality:ultra fine->more->optimize structure first->more->algorithm: Quasi-Newton-> keep everything as default (as described in this paper)
->number of steps for each strain->4
->max strain amplitude->0.003 (those two parameter I keep as default, not mentioned in the paper)
-Energy->COMPASS->forcefield assigned-> quality ultra fine (as in the paper)
->summation method->electrostatic->Ewald->van der Waals->Ewald (as in the paper)
Results that I'm getting are attached in txt file. What I have noticed is I'm getting different 'independent elastic constants' than reported in the paper in table 3.
Any reason for that?
Also for Reuss, Voigt, Hill for Bulk and shear modulus some of the values are negative, not sure if that's correct
Thank you in advance for any suggestions,
Monika
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
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