How to calculate the RMSD value of a multiple regions using VMD?

How to find out the problem of VMD software when i run it?

Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...

22 February 2021 8,211 3 View

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View

How can I make a center of mass vs time graph?

I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...

04 February 2021 5,774 1 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

What is the best way for mobility estimation in GROMACS?

I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...

19 January 2021 531 3 View

How to script VMD tcl within bash script?

Greetings, I want to run a vmd script within my bash script. I am using the text only version of VMD for linux for my windows terminal ubuntu subsystem and I would like to generate code within my...

16 January 2021 192 5 View

Recognition of Molecules from a file containing molecular dynamics trajectory?

Can anyone recommend a good code/software/implementation to identify the change of molecules (bond creation/break, number of molecules at a given timestep, etc.)? I am currently working with XYZ...

12 January 2021 1,655 4 View

How to increase GPU usage during MD simulation?

The GPU usage percentage of my Nvidia Quadro K3100M does not exceed 10% during running MD simulation of protein of 252 residue length using VMD/NAMD software. Any one can provide advice on how...

08 January 2021 7,594 3 View

How to solve "Too many atoms in a patch" error?

Hi all, I was trying to run a simulation in NAMD but encountered the following error: FATAL ERROR: CudaTileListKernel::buildTileLists, maximum shared memory allocation exceeded. Too many atoms in...

01 January 2021 6,491 3 View

Can i use MM-PBSA to calculate the binding energy of a glycan ligand? ad how?

I have a protein-ligand (glycan) complex and want to do an MM-PBSA analysis using AMBERTOOLS after doing MDS (NAMD). What are the files necessary I should prepare for glycan? Note: I used...

30 December 2020 2,658 2 View