Jaffri. Re

12 Questions 11 Answers 0 Followers

Questions related from Jaffri. Re

How to make the acidic form of MFI Zeolite for MD studies?

Dear MD users, I would like to draw the acidic form of MFI Zeolite, substituting Si with AL and adding a Silanol group. I used Materials Studio to make the changes to the structure and build a...

26 February 2025 8,303 0 View

There were 2136 inconsistent shifts. check your topology ( Gromacs) ?

GROMACS version: 2022 Dear Gromacs users, I am studying the diffusion of water in MFI zeolite. The simulation is done without any errors. However, When I want to calculate the diffusion...

14 November 2024 1,001 3 View

Does simulation time effect on diffusion coefficient of water in zeolite at low water contents?

Dear Researchers, I am performing a simulation regarding the diffusion of water molecules in an MFI zeolite structure. The parameters are exactly obtained from a high-quality paper. I first did a...

04 November 2024 525 1 View

How to unsure that water molecule in the simulation box is in gas phase or liquid phase?

Dear MD users, If we consider a simulation box consisting of water and other things (polymer or CNT, for example), how can we determine whether the water molecule is in the gas or liquid phase?...

25 October 2024 7,228 3 View

How to run gromacs on HPC?

Dear gromacs users: I would like to use the cluster to run my simulations. Indeed this is the first time I am using cluster. I have prepared the md.tpr file but don’t know how to run the mdrun...

15 October 2024 6,223 5 View

Does the shape of zeolite effects on diffusion coefficient in molecular dynamics?

Dear researchers, I want to calculate the diffusion coefficient and MSD of water in MFI zeolite using molecular dynamics simulation. I chose two different Pristine MFI supercells, similar in...

11 October 2024 9,410 5 View

How to obtain forcefield parameters for H2 and O2 in OPLS forcefield?

Dear MD users, I am trying to simulate diffusion of H2 and O2 in Zeolite structure. I have the OPLS parameters of the Zeolite framework but how can I have parameters for O2 and H2? I am a bit...

30 September 2024 3,559 1 View

Non bonded interaction is larger than table limit in GROMACS?

Dear Gromacs users, I am performing a simulation setup consisting of water and zeolite MFI. The simulation setup is shown here in this post. When I run nvt and npt I encounter an error which is...

23 August 2024 9,770 6 View

Inconsistent shift in the simulation of Zeolite in Gromacs?

Dear MD users, I would like to perform an MD simulation of water diffusion in FER Zeolite using gromacs. in the first step, I downloaded in CIF file of FER from IZA and extended in (3*3*6)...

16 August 2024 3,875 1 View

How to draw polymer chain in tube form in vmd?

Dear all, I would like to draw my polymer chain like the picture I attached here. I used Graphics -> representations-> Drawing style -> Tube But, when I choose Tube my simulation box disappears...

29 December 2021 8,668 3 View

How to calculate collective diffusion coefficient in gromacs?

Dear MD users, I would like to calculate the collective diffusion coefficient of water molecules into the zeolite structure using Gromacs. It is easily possible to calculate self-diffusion using...

01 January 1970 8,259 2 View

How to remove a list of atoms by index in materials studio?

Dear MS users, I want to modify a supercell structure. In this case, I want to remove a list of atoms by index. For example, I want to remove [1,4,8,12,56,45] indexes. how can I do that? Or do...

01 January 1970 6,004 2 View