Christos Eu

7 Questions 4 Answers 0 Followers

Questions related from Christos Eu

Protein leaving one face of water box and reappearing on other side seems to affect analysis of NAMD simulation?

I am simulating a protein-protein complex and have placed the complex in a minimal water box with 15 Angstroms of distance from the end of the box. Now that I have completed the simulation, I ran...

04 January 2023 2,819 3 View

Is there a TCL script to perform principal component analysis (PCA) on a dcd trajectory?

I am using tcl scripts in VMD to calculate several properties of my simulation including RMSD, RMSF, H bonds, etc. However, I would like to perform principal component analysis (PCA) on my...

21 December 2022 9,222 0 View

Are there any maintained alternatives to Docear?

I have been searching for a reference manager and mind mapper tool, and the only one I have found is Docear. It seems like an incredible tool, but I am a bit concerned with using it as it is no...

14 November 2022 6,256 1 View

Is it faster to use bigdcd or to wait for a large trajectory to load into VMD for analysis?

I am using a Windows 10 computer and have installed VMD 1.9.4a53 since it is 64-bit and allows for larger simulation files to be loaded without crashing. However, is it faster to use bigdcd when...

12 October 2022 6,653 0 View

How to run local python code on files located on a mapped network drive?

I have run several molecular dynamics simulations using NAMD on a supercomputer, and I have transferred the trajectories to mapped network drive on my Windows 10 computer. I am unable to transfer...

01 June 2022 9,483 0 View

How do you analyze/plot multiple NAMD trajectories simultaneously?

I have been using QwikMD/NAMD to run MD simulations, and for each setup I run three simulations to have replicate results. Now, I would like to plot the results from the three trajectories, along...

19 May 2022 4,835 3 View

How do you calculate the free binding energy of a protein-protein interaction from a molecular dynamics simulation?

I have used QwikMD/NAMD to run a simulation of a system containing two protein chains, and I would like to calculate the free energy of the binding interaction. How would I go about doing this?...

03 May 2022 4,237 4 View