What is an apolar molecule? There is a special category in MARTINI coarse grained force field.
Dear all, I have a quarry regarding the temperature effect on the pi-pi interaction. Thank you
04 May 2018 4,220 1 View
Dear all, Can anyone refer me the literature about the effect of the pi pi interaction on the free energy of solvation. Thank you
04 May 2018 8,181 0 View
What are the advantages for the algorithm based on compactly supported orthonormal wavelet bases
10 November 2016 6,918 0 View
Atime-series database stores sequences of values or events obtained over repeated measurements of time (e.g., hourly, daily, weekly). Examples include data collected from the stock exchange,...
10 November 2016 9,691 3 View
I need to find order of convergence of a method How to find it
10 November 2016 544 2 View
how we can calculate order of convergence of hankel transform?
10 November 2016 9,110 0 View
10 November 2016 1,365 1 View
I want to ask one question related to data processing in Topspin. I done 10 1-d diffusion experiments. Now I have to find the area under one peak(in all spectra) and then I have to plot it. After...
04 May 2014 1,859 4 View
I have to study diffusion by gromacs. I want to calculate full tensor of diffusion coefficients. I am using "g_msd -ten". But it is giving me only one value. I want to ask that my command is...
02 March 2014 4,775 4 View
I am using coarse grained builder in VMD software. In residue based CG mapping, there is an option for bead definition. I am confused as to how to proceed and appreciate any suggestions. Thank you.
11 December 2013 7,661 1 View
I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...
08 August 2024 8,329 0 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
I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...
30 July 2024 6,420 1 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
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 Siesta Users, I installed Siesta 5.0.1 and I want to use Grimme's D3 correction. According to the 5.0.1 manual, I could use a few parameters to include the D3 correction in the...
27 July 2024 5,748 0 View
It has been long known that EDC carbodiimide and NHS easter's half life agains hydrolysis are highly related to pH. However, very surprisingly, not yet found a paper giving a table/chart of their...
25 July 2024 8,738 0 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 run mechanochemical reactions that involves the use of a large amount of catalyst (1:1 molar ratio to the reactant). When I try to understand the effect of amount of catalyst on the reaction, I...
23 July 2024 9,938 1 View