How to perform adsorption simulations in Gromacs?

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How to install VMD in ubuntu (Windows 10)?

I have already installed GROMACS in ubuntu (Windows 10), but now I would like to install VMD software in ubuntu (Windows 10), unfortunately I haven' t achieve it.

22 September 2020 10,140 3 View

Which software would you recommend me to use between GROMACS and NAMD?

I have a system where there is a protein that interacts with different surfaces (copper and graphite). I am interested in adsorption phenomenon.

19 September 2020 2,812 2 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

Absorption coefficient of methane?

Hello, Can anyone provide me with the absorption coefficient of methane gas at 7.7 um? Any reference?

06 August 2024 980 5 View

In the presence of VERY high concentration (1000 ppm) of silicon, the adsorption isotherms of arsenic are showing anomalous trends, why so?

I conducted an adsorption experiment of arsenic on soil in the presence of different doses of silicon as competing ions to see the effect of silicon on arsenic adsorption and desorption. I took 5...

03 August 2024 6,500 3 View

How to restart MD without using checkpint file in GROMACS?

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

How to prepare a molecule for molecular dynamics calculations?

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

Wrong out put for gmx x2top?

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

How to calculate pseudo order kinetics?

I know the rate law. But for my photo-catalytic experiments, first 90min is adsorption (dark) and next 150min is under UV light (total 240min). How to remove the adsorption part for calculation?...

21 July 2024 8,807 6 View

Why binding energy is in positive number after performing mmpbsa?

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

How to resolve ‘[ atomtypes ] Invalid order for directive atomtypes’ error in Gromacs?

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

Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

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