I am trying to do a dft calculation in gromacs but don't know the code. Can anyone provide me the detailed code of the same.
What kind of rock should be targeted to prepare secondary oxygen isotope standard? The mineral of interest is quartz.
27 April 2024 6,250 2 View
if the fugacity of S rises or fugacity of O drops, is it possible to precipitate magnetite and pyrite from a same hydrothermal fluid? Is there any case study?
04 March 2024 7,494 5 View
These larger benthic foraminifera (probably) are very well preserved in the Miocene sediments. Please help to identify the species
15 February 2024 7,471 2 View
Hi everyone, we use traditional techniques such as simple water soaking or methods using hydrogen peroxide (H202) or washing-soda (Na2CO3) for disintegration and extraction of foraminifera and...
10 October 2023 2,068 9 View
How did climate conditions influence the formation of limestone?
10 August 2023 1,371 0 View
10 August 2023 985 0 View
How to read a .mat file in eeglab (addon in matlab)? An error is generated: EEGLAB error in function pop_loadbva() Please suggest.
21 June 2023 6,950 4 View
Secondary ion mass spectrometry: basic concepts, instrumental aspects, applications, and trends By A. Benninghoven, F. G. Rudenauer, H. W. Werner · 1987 ISBN:9780471010562,...
30 May 2023 1,295 0 View
Could you please help me to sort out one Gromacs problem? When I run gmx dssp (Gromacs 2023) command, it generates .dat file (e.g. ss.dat) as output. (.xpm is not working in Gromacs 2023). How do...
13 May 2023 3,688 13 View
What are the processes that can be implemented to ensure the validity of the application of the inclusion and exclusion criteria in a literature review?
18 December 2022 9,571 1 View
Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...
07 August 2024 266 3 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 2,597 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 3,083 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 672 3 View
Hello! I am trying to calculate the sumatriptan molecule, but it has been counting for five days and it does not stop. It seems to me that it is too long and I am doing something wrong. Please...
25 July 2024 3,364 5 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 365 4 View
Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...
21 July 2024 1,631 0 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'm trying to study the effects of introducing vacancy defects in my material. If I optimize my structure and find the lattice parameter before introducing vacancy, should I again optimize my...
18 July 2024 1,794 2 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