13 Questions 4 Answers 0 Followers
Questions related from Yeongkyu Lee
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....
02 February 2019 7,389 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"...
12 December 2018 9,159 0 View
Is there any procedure that I can adapt? or If there's some paper, please let me know. With my respect
11 November 2018 8,178 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...
10 October 2018 6,992 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...
10 October 2018 8,553 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 =...
10 October 2018 575 4 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...
09 September 2018 5,194 0 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...
09 September 2018 10,030 2 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...
07 July 2018 5,147 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...
03 March 2018 786 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
02 February 2018 9,790 2 View
I am currently using gromacs and VMD. I tried energy minimization of structure from gromacs and I tried to figure out how the structure was changed. Surprisingly, the structure was divided into 4...
01 January 2018 3,429 7 View
Does anyone knows solubility of water-ethanol mixture? Chemical I am using consists of soluble in water and insoluble in ethanol. Please help me.
08 August 2017 369 3 View
