Is there any procedure that I can adapt? or If there's some paper, please let me know.
With my respect
Dear researchers, I am using gromacs for molecular dynamics simulation. These days, I am working on lennard jones fluid. In lammps, it is easy to use reduced unit by just set the parameter as 1....
01 February 2019 7,412 2 View
I want to make shell script for calculating rdf. I want to make a lot of rdf.xvg files for each time step. Here's my approach. #!/bin/bash for i in $(seq 1.1 .01 30.0) do echo -e "OH2\nOH2\n"...
11 December 2018 9,200 0 View
I have 50 ns simulated bulk water system. For analysis, I want to calculate tetrahedral order parameter q. I am using gromacs, and I know the command "gmx hydorder". However, I don't know how to...
09 October 2018 7,029 3 View
I have configuration simulated with gromacs, NPT for 50 ns. During analysis, I got problems. 1. tetrahedral order parameter q 2. Double donor and single donor configuration division(reference of...
09 October 2018 8,574 0 View
I am trying to calculate voronoi volume of a water surronded by nearest oxygen. This is my code. from numpy import * import glob box = 3.73014 list_of_files =...
09 October 2018 594 4 View
I installed drude implementation files from charmm website. Here's URL: http://mackerell.umaryland.edu/charmm_drude_ff.shtml. On my linux server Downloads directory, I did the procedure 1. git...
08 September 2018 10,061 2 View
I am recently using gromacs to simulate bulk water. I modified existing swm4-ndp.itp file and did the 10bs NPT after 200ps NVT. But the problem is result. Energy, density and volume is nice, but...
08 September 2018 5,222 0 View
Does anyone know where could I find polarizable water model force field and coordinate file? I looked it up in martini website, but there's no one-bead polarizable model. Rather, they suggest 3...
06 July 2018 5,173 0 View
In the lattice model in soft matter physics, average number of solute and solvent pair is calculated by = zNtotV(1-V) where z is coordination number and V is volume fraction for the solute...
02 March 2018 812 0 View
I want to insert molecules inside the wall. Configuration is like below. I want to put some ions inside the wall surrounding polymer. Please help me. YK Lee
01 February 2018 9,832 2 View
I tried four trials of the same Copper Phosphides sample in Alkaline medium ( 0.5M KOH) with Hg/HgO reference electrode and Pt as counter electrode. I used 0.001 V/s scan rate for first three...
10 August 2024 3,629 1 View
How can I determine a good adhesion strength range for coatings on polymer surfaces, such as DLC on polymer substrates? Is there a specific threshold for adhesion strength (from T-peel tests)...
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How do interactions between the biosphere, the carbon cycle, and the water cycle impact global warming and interaction between the atmosphere and the hydrosphere?
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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
Global ‘Weather’ has stopped, as ‘aqua thermionic instituted by the ‘Global thermo atmospherics has instituted global thermodynamics of 120º C + and thus all waters are, or have boiled into a...
06 August 2024 8,716 0 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?
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Molecular docking software/ websites?
02 August 2024 8,704 7 View