MD simulation data using MDplot in R packages?

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

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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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

SAMEE ULLAH

https://rdrr.io/cran/MDplot/man/hbond_ts.html

https://rdrr.io/cran/MDplot/man/rmsd.html

https://rdrr.io/cran/MDplot/man/dssp.html

Kalyani Dhusia

I needed to know how can I use my data instead of predefined dataset in R

R C Dash

Use gromacs tool ( like gmx cluster g_rms) to analysis and use the output for plotting in MDplot. the examples are in /MDplot/inst/extdata folder.

How can I get my gromacs plots to mdplot... that's my question specifically

Use gmx cluster and g_rms command to get the .xvg file and usere that xvg file. then you have to modify the the xvg file for MDplot.

Rimon Parves

instead of using R package , you can use MDtraj,Pytraj,Cp traj for more analysis. They support wide array of data

Thanks!