21 Questions 32 Answers 0 Followers
Questions related from Mohammad Rezayani
Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...
25 July 2024 317 4 View
Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...
16 July 2024 4,558 1 View
Dear ResearchGate Community, I am currently working on simulating the zeolite (MFI, FER, TON) structure using GROMACS, but I am facing challenges in finding the appropriate force field parameters...
08 April 2024 6,407 3 View
Dear Martini 3 users: I would like to define beads for the attached structure but I have no idea how to define appropriate atoms and bead types, especially for the C in the middle with 4 carbons...
01 January 2024 4,145 1 View
Hi all, I am simulating a nano-tube using GROMACS. After NVT or NPT level some bonds are removed in VMD. What is the reason? Also, I got the structure using gmx trjconve, but the bonds are still...
11 February 2023 1,686 5 View
Dear all, I am doing simulation for a polymer/water system. I would like to do RDF and coordination number analysis for this system. I got results like in figure I attached here. I know the...
09 November 2021 9,125 3 View
Dear all, I want to calculate residence time in Gromacs. For this purpose, I need to calculate residence time auto correlation function. Is there any way to calculate it in Gromacs? Or, is there...
23 June 2021 7,475 0 View
Hi, I want to calculate water residence time near N+ as a fixed ionic group in my polymer system. Is there any direct way to calculate average residence time of water near N+? If not, could you...
20 June 2021 3,732 6 View
How can I calculate Hydrogen bond life time in Gromacs between two groups like water-water and water-specific group in a polymer?
11 November 2020 2,561 3 View
Dear all I want to simulate a system containing polyelectrolytic and water. I would like to do annealing for more relaxation. But, I dont know if annealing process is better to do in NVT or...
31 October 2020 958 1 View
Dear all Is it possible to calculate friction coefficient in Gromacs?
06 October 2020 2,554 2 View
Dear all, I want to simulate a polyelectrolyte with its counterions( five chain and 200 ions). I did distance restrain between ions and (N+) in the polymer chain. In NPT level my system is not...
14 August 2020 4,767 4 View
Dear all, I want to distance restrain for an ion and its associated residue. There are 5 polymer chain and 200 ions( 40 for each chain). I made restrain.itp for my desire atoms and their...
11 August 2020 4,628 1 View
Dear researchers I want to run a Gaussian MP2 job. I have defined 6 cores for calculations but after houres it declined to 2 cores with the following warning: Disk-based method using O(N**2)...
10 July 2020 2,038 3 View
I want to simulate polyelectrolyte of PPO . I inserted counterions into the simulation box and changed their position near the protonated group with position.dat file. but after minimization and...
20 May 2020 5,592 4 View
Dear all I want to simulate water diffusion in polymer matrix using Gromacs. I would like to know about system size effects. Then, I chose system with 10, 20 and 30 chains. In all systems, water...
01 January 1970 9,894 4 View
Dear all, Diffusion coefficient of water especially in porous medias like polymer is multiple of translational and rotational diffusion coefficient (DT + DR). In Gromacs we can have just...
01 January 1970 9,565 6 View
Dear all I want to analyze cluster size of water in polymer. in an article, there were a figure(mentioned here). But, I can not understand the figure. There is number of molecules VS cluster size...
01 January 1970 8,380 2 View
Dear all I want to calculate diffusion coefficient VS time in Gromacs (like figure below)to know at what time the system reaches to a stable diffusion state. What is the best way to do such...
01 January 1970 523 8 View
Dear all I want to calculate coordination number of water around N+ group. I first calculated area of RDF to first minimum and it gave me a wrong coordination number( my RDF is correct) . Then I...
01 January 1970 5,919 1 View
Dear all, I want to calculate ACF of radius of gyration using gmx gyrate. I used the following command: gmx gyrate -f npt3.xtc -s npt3.tpr -o gyrate.xvg -acf gyrateacf.xvg -n molindex.ndx -b 0 -e...
01 January 1970 9,578 4 View
