In the study of swelling clay and factors affecting swelling.
Hello, I am in the process of making a predictive nonlinear model for my data with one dependent variable and 3 independent variables. I am currently using SPSS and R but the best model i have at...
04 May 2019 1,827 3 View
Hello all, i would like to generate an .itp file using clayff force field with gromacs. i tried the gmx x2top -f .gro -o .itp -ff command but got error message In command-line option -o...
11 December 2017 7,381 3 View
Hi all, i am currently working on montmorillonite clay. i am using Gromacs, clayff and vmd. i got a unit cell from an online data base but would like to create up to 6 or 16 unit cell model. also...
11 December 2017 3,621 4 View
HI all, i am currently carrying out a gromacs simualtion and the simulation has been going on for over 20days because the system is heavy but i will like to know how to check the current state of...
09 October 2017 1,470 7 View
Hi all, i am presently working with a system containing NaCl and i added some Calciumchloride to see the influence of change in cation. Now i have my results but i'll like to know how i can study...
08 September 2017 2,010 3 View
i want to extend a completed simulation and i need to increase the temperature. from the documentation i saw this "If you wish/need to change .mdp file options, then either grompp -f new.mdp...
07 August 2017 1,839 11 View
Hello everyone, i am currently working on the effects of temperature on a system but with my current mdp setting the results are not looking realistic. Curently 300K and 600K are giving the...
07 August 2017 3,240 4 View
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
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
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...
24 July 2024 367 4 View
I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...
19 July 2024 4,120 5 View
I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...
17 July 2024 9,897 4 View
i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...
17 July 2024 6,216 1 View
Hello everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...
16 July 2024 7,205 2 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...
15 July 2024 4,590 1 View
Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...
08 July 2024 4,724 4 View
