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 7,304 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 8,965 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 6,779 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 8,496 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 523 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 9,901 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 5,039 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 5,054 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 722 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 9,661 2 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View