Questions tagged [vmd]

Questions about the VMD software.

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6
votes
0answers
87 views

How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
6
votes
1answer
194 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein here. The trajectories are from my Gromacs simulation. Firstly I use ...
6
votes
1answer
72 views

Secondary structure information at each frame in a VMD trajectory

I am trying to write a tcl script to measure percentage helicity at each frame of a VMD .dcd trajectory. I found the following discussion on the VMD mailing list to calculate the secondary structure ...
7
votes
1answer
119 views

How do I build and run a simulation of water molecules in NAMD?

So, I have started to learn NAMD because I need that for a project I will be doing in the next couple of months. I have some prior experience of MD with gromacs. I thought that since NAMD has a GUI ...
8
votes
2answers
166 views

File type to write bond information

I have an xyz file upon which after processing in Python, I determine bonds between different atoms. What would be the correct file type that I can write to visualize this bond information in VMD?
11
votes
2answers
396 views

How to include individual PBC box dimensions in xyz file format compatible with VMD

I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this: ...
11
votes
2answers
391 views

Recalculate atom positions to account for periodic boundary conditions

I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
11
votes
1answer
230 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...