Hi, i working with Materials studio, I want use materials studio to do this work " Molecular Dynamic (MD) simulations of studied inhibitor in this study have been carried out in a simulation box with periodic boundary conditions taking Materials Studio. The iron crystal was imported and cleaved along (110) plane and a slab of 5 Å was employed. The Fe (110) surface was relaxed by minimizing its energy with the help of smart minimizer method. Fe (110) surface was inflated to a (10 × 10) super cell in order to provide a large surface for the interaction of the acrylic acids. A vacuum slab with zero thickness was built. A supercell with a size of a=b=24.82Å c =25.14Å, consisting of 500 H2O and molecules of tested inhibitors was created. The simulation was carried out in a simulation box (24.82 × 24.82 × 35.69 Å3) using discover module with a time step of 1 fs and simulation time of 500 ps performed at 298 K, NVT ensemble, and COMPASS force field." Could anybody help to do this study?
Hi, this is getting way too complicated. Can I reiterate that Materials Studio does not support the DMol3 scan_pes task, there is no support for it, and we never promised that it works in any documentation. Instead, we have a very powerful set of scripting tool, which allow you to do many more things than simply constraining single bond lengths and then having to sort through the outmol file in detail. I have written an example script that does exactly the calculation you are looking for and returns a study table with a summary of the results. The script and an appropriate input file is attached, feel free to add any particular property that I might have missed. All the best, Felix
Hello Dear MS users, I have a question about homopolymer building...when i created isotactic polypropylene chains using MS Build-> Homopolymer->library->Olefins->propylene, everything is OK. But when I sketched propylene with myself and Built it as repeat unit, and created polypropylene chain by applying 1-library->current project 2-Repeat unit->my sketched propylene repeat unit 3-Tacticity->isotactic But the final structure is not isotactic polypropylene and have different tactility!!! Would you please tell me why these two results are different? I think this problem can be very important when a user wants to create an isotactic polymer, that its repeating units is not in the MS library.
I am doing PhD ( mechanical engineering ) on impact analysis of Graphene reinforced polyurethane nanocomposite using Accelrys Material studio 7. For impact analysis constraint is very very important. Can anybody discuss various type of constraint used in material studio???when we used atom,length and lattice constraints??? During impact analysis is it possible to give velocity on the impactor or striker in material studio????
I am trying to calculate the solubility parameter for a single chain of polymer.The above expression is given in a reference(link).Could someone tell me how to calculate Es and Eb given in the equation.Es the single chain energy; Eb the energy of the same chain in periodic system; Vc the volume of the cell in cubic angstrom, C the unit conversion factor. How do I calculate Es and Eb from the trajectory file of the dynamic run?
Thank you so much for your time and consideration.
The easiest would be to run Forcite Cohesive Energy Density task, which will do this calculation for you.
In principle you could simulate a single molecule in vacuum at a given temperature, and obtain Es as the average total energy. Then run a liquid simulation at the same temperature and obtain Eb as the average total energy per molecule. Since the temperatures are the same, the kinetic energy cancels. You’ll need to divide by the volume per molecule to obtain the cohesive energy density.
In practice for small molecules the vacuum energy equals the intramolecular energy in the liquid, and you can obtain Es – Eb directly as the average intermolecular energy, without simulating the vapor. For polymers simulating the vapor is not realistic as experimentally they decompose.
Below are two posts with scripts to build icosahedron and dodecahedron shaped nanoclusters. The basic idea is to carve the required shape out of a block of material. You could something similar for your nanowire.
Hi every one I used Amorphous Cell to bulit cell containing 100 molecules and the geometry optimization has been performed after construction.Then the system went through NVT dynamics in Forcite with thermostat Nose.However,lots of molecules went out of the cell after the dynamics finished, so I think the boundary condition does not work,but I do not know what is wrong with my caculation.I come across the same problem when using GULP for dynamics.Picture is finall frame.
Did you check "Recalculate atom visibility every frame" on the Animation Options dialog? This will effectively change the display style of the Lattice to "In-Cell" for each frame, and hence keeps atoms in the box during the animation.
Hi, I'm new here. I have a question regarding geometry optimization-Forcite module. I tried every forcefield available in the module but still the end result is not converge after the iteration finished. Increasing the iteration is also not working. I'm trying to find g(r) using this module. Thank you
When you choose a forcefield you need to do so carefully, as it needs to describe the potential energy surface of your structure reasonably accurately. In general COMPASS is usually the first choice, but if you have some exotic structure containing say metal complexes then Universal might be a better choice. Your Geom. Opt. may fail to converge, because the forcefield does not provide a good description of the potential energy surface. Usually when that is the case then there are warnings or errors messages about missing or automatic parameters and / or the resulting optimized structure is far from the experimental one. If you use rigid bodies and they are internally strained this can result in a failure to converge. Also if the tolerances are too tight then they may never be met! However, if may be that you can ignore these messages, but do so with caution. i.e. check to see if the final structure is reasonable; for example are bond lengths, cell parameters, etc about right? Are rings that should be planar actually planar or are they distorted etc.
BTW Normally the g(r) is computed from a trajectory produced in a dynamics run otherwise you will not take into account temperature effects and will be difficult to compare to experiment.
Dear All I have recently updated Materials studio 2016 to my windows machine. We have a licence for CASTEP and ONETEP as well. It works absolutely ok with CASTEP using single core along with parallel calculations but with ONETEP, It does not work for even a single machine. Please update me what to do. here i have copied the warning .............
Job started: 27-04-2016 10:41 (+0100)
License checkout of MS_onetep successful
Reading parameters from file "Al.dat" ...... done
Checking processes and threads... Running with 2 MPI processes. There are 2 MPI processes running on the same node as the root process. This binary does not support OpenMP threading. ... done
'''''''''''''''''''''''' ONETEP terminated abnormally due to the following error:
Error in parallel_strategy_list_overlaps: spheres exceed cell size. ... detected on MPI rank #0. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ONETEP execution aborted
Checked out license feature: MS_onetep <v2015.10> [for 4804:219863:2:THE UNIVERSITY OF BOLTON] (1 copy)
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
The error is described in the lines that say "error". OpenMP is a warning. The error comes from ONETEP's dislike of small cells. If atom-centered spheres overalp with their periodic images, ONETEP cannot operate. This code is designed for large systems; in fact, the crossover in terms of performance between ONETEP (linear scaling) and CASTEP (quadratic to cubic scaling) happens for systems with hundreds of atoms. Smaller systems are faster with CASTEP. Anyway, if you want to use ONETEP, please make a bigger supercell - look at atomic radii in ONETEP setup options to get an idea of how big it should e to avoid spheres overlap. Cheers
Dear All, I have used COMPASS force field to estimate the cohesive energy density(CED) of ethanol.It gives a value close to the experimental result.I have also checked this with the Dreiding potential,the result predicted is not close to the experimental value.Could someone explain why there is a difference in result? Is it necessary to use COMPASS for predicting liquid properties?
COMPASS is fitted to experimental CED data, so it is likely that it will do a better job than Dreiding, which is fitted to crystal structure and sublimation energy. Moreover Dreiding does not provide charges, and the result depends on the way these were calculated.