I have two groups of atom of moving particles. So how can I put the distance constraint, without making them rigid.
How can we access the information on the atom indexes involved in a given collective variable. I can see that it is possible to access this information in colvar and analysis classes. But is it...
03 April 2019 7,259 2 View
1. What should be non-bonded interaction parameter for the atoms of the wall? 2. How to ensure its correctness? Thanks
10 November 2016 6,454 0 View
I am simulating a system consist of ~2000 atoms. I have checked on different machines but the result is same. Any guidance will be helpful.
03 April 2016 2,272 6 View
A simple GPU algorithm for finding triplet correlations accelerated on CUDA. Please follow the link.
04 May 2015 2,963 0 View
Please explain with proper reasons... Thanks.
01 February 2015 6,758 7 View
please explain .
01 February 2015 6,067 0 View
What are the general equations for a conic selection. I want information about the atoms present in a conic volume of given radius and height. Please explain.
01 February 2015 1,864 3 View
In thiosulphate, two sulphurs have oxidation state of -2 and +6. (as per suggestions). Sulphur bonded to three oxygen is considered to have +6 (Sulphur A) and other sulphur has -2 (Sulphur B)....
01 February 2015 4,473 7 View
I am using Nvidia's K20x cards on my machine. I am facing some problems in using lammps gpu enabled version upto its full efficiency on GPU-node. The main role of the gpu is to save the time...
01 February 2015 3,795 1 View
Nitration of Aniline in Conc. H2SO4 and HNO3, we can understand the formation of both para and meta nitro aniline. But what is the reason for the poor yield of ortho nitro aniline?
10 November 2014 2,146 7 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 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
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 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
Hello, We found three packages of Illustra™ MicroSpin™ G-25 columns in the cabinet of an unused lab. They are very old but have never been opened. I have never used this kit before, and I couldn't...
25 July 2024 4,927 3 View