How to convert reduced units to actual units when an MD simulation is carried out?

I have done simulations of colloidal suspensions where I have converted the actual units to reduced units for timestep, density, temp etc. From simulation data, I have calculated equilibrium...

31 December 2016 6,722 4 View

What is the difference between particle distribution and radial distribution function? Is there any difference between them?

08 September 2015 4,836 1 View

Can anyone explain to me the Non-Gaussian Parameter (alpha(t))? How can I calculate it using MSD?

06 July 2015 2,417 4 View

Can anyone provide me matlab code for sine fft and inverse sine fft ?

I'm working on Ornstein Zernike Equation, to study the effective interactions between charged model colloids. To calculate the structure factor for colloids I wanted to use fourier transforms.

31 December 2014 3,781 11 View

When do you say that the molecular dynamic simulation has been converged? How do you check the convergence of a MD simulation?

I am working on MD simulations of colloidal supensions. I would like to find out the convergence of my simulation. How do I knew that my system in MD has reached convergence?

08 September 2014 6,621 4 View

Can anyone tell me what would be the minimum temperature fluctuations considerable in molecular dynamics simulation during the equilibration?

During the equilibration of colloidal system using MD simulations, what would be the minimum considerable temperature fluctuation?

07 August 2014 9,830 7 View

How can we read and write the data from a text file in matlab where I can use this data as my input?

I had a large textfile with about 1001 rows and 5 columns of strings in 1st row and numericals in remaining rows. I would like to read this data from file and would like to use it as input for my...

05 June 2014 3,367 9 View

How can I solve the Ornstein Zernike equation for two component systems using MATLAB?

I want to solve OZ equation for simple liquids using MATLAB.

01 February 2014 8,351 1 View

How to calculate direct correlation function between colloids?

I would like to calculate dcf between colloidal particles, which would help me to calculate the effective potential between colloids.

11 December 2013 820 9 View

How to model and simulate patchy colloid?

I would like to model a patchy colloid which has directional interactions..

05 June 2013 2,704 5 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 June 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

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

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

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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View