How to calculate tetrahedral order parameter in gromacs?

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How to use reduced unit in gromacs?

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

Can I make shell script for gmx rdf?

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

How to generate supercritical CO2 in gromacs?

Is there any procedure that I can adapt? or If there's some paper, please let me know. With my respect

10 November 2018 8,116 0 View

Tetrahedral order parameters and local water configurations?

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

How could I calculate voronoi volue of water?

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

Does anyone knows how to install drude implementation files for gromacs?

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

Does anyone know how to simulate swm4-ndp in gromacs?

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

Polarizable water model ?

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

Could anyone help me inderstanding Soft matter lattice model?

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

How can i insert molecules inside in gromacs?

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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

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