How can I convert .lib to .off file format of MD force fields to use in material studio modules??

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Boundary condition for a combined system including crystal and amorphous structure?

Dear researchers, I want to perform a DFT simulation on a combined system including a crystal (MnO2) and an amorphous (water) structures. How can I apply boundary condition on it? Thank...

01 February 2019 4,226 1 View

Can anyone send me .CIF file of delta-MnO2?

Dear all, I am trying to find Crystallographic Information File (CIF) of delta-MnO2 but unfortunately I could not find that. Can anyone send me .CIF file of delta-MnO2? Regards, Mina

11 December 2018 3,171 3 View

How one can get pdb format of a molecule from X-ray diffraction?

Dear all, I need the pdb structure of porcine skin gelatin or collagen, but I coul not find it anywhere, even in PDB data bank. How can I extract PDB structure file of this material from XRD...

10 November 2018 9,375 4 View

How to assign atomic charge in PCFF or COMPASS force fields?

Dear all, I am using msi2lmp to build my lammps data file with PCFF force field. I have been confused about the atomic charge assigned by PCFF. Considering the concept of bond charge increment, I...

06 July 2018 9,884 0 View

How can I apply periodic boundary condition in two of three dimensions in sorption or forcite of material studio?

I want to implement a sorption task with material studio. PBC in two dimensions of x and y is favorable. How can I perform this in material studio?

06 July 2017 6,173 0 View

What are the diferences between nanoparticle@MOF core shell structure and MOFs doped with nanoparticle?

Are they the same? or different?

11 December 2016 6,055 0 View

I have get this error when i calculated the geometrical optimization for prco3, it takes 12 hours until gives this message in the outputfile?

Fatal error in MPI_Allreduce: Other MPI error, error stack: MPI_Allreduce(1628)......: MPI_Allreduce(sbuf=000002459254A180, rbuf=000002459F86A140, count=4851, MPI_DOUBLE_COMPLEX, MPI_SUM,...

09 August 2024 7,615 1 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

What is the prepared reference material that can be used in inductively coupled plasma optical emission spectrometry (ICP-OES) to measure REE and U ?

What is the prepared reference material that can be used in the ICPE-9820 Shimadzu Japan instrument, which employs inductively coupled plasma optical emission spectrometry (ICP-OES) to measure...

06 August 2024 1,896 1 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How effective is the Citi Bloc standard basket in enhancing the accuracy and comparability of international construction cost assessments?

Citi BLOC Standard Basket Definitions: A standardized unit representing a fixed basket of construction materials, labor, and equipment costs priced in various cities. Purpose: To create a common...

04 August 2024 8,997 1 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View