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

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How to build a gold nanocluster computationally?

Hello all, I want to computationally design design Au25 nanocluster with attached ligands. I have designed the icosahedron metal core using Open MD. Now I need to attach six -S-Au-S-Au-S-...

23 May 2024 2,580 0 View

Fatal error: Syntax error - File tip4pew.itp, line 5 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype?

Hello all, I want to run a Molecular dynamics simulation by using Gromacs and OPLS AA force field. I'm getting the above error when I tried to run the energy minimization step. Now I don't...

20 June 2023 1,216 3 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View

RMSD of Protein ligand complex is higher than the apo form.Why?

I have performed a 100 ns md simulation for protein ligand complex .The result generated is found that the complex RMSD is higher than the Apo form.What could be reason for this ? Could anyone...

24 June 2024 9,049 3 View

What possible issue am I facing in this Alchemical FEP calculations using NAMD?

I am trying to run my tcl script for NAMD. Running separate MD simulation for each forward and backward runs. Forward run is fine however backward.inp abruptly terminates showing output only till...

17 June 2024 861 1 View

What could be the possible reason of a sudden fluctuation in a stable RMSD plot of a protein-protein simulation?

I have run MD simulation of a protein-protein docked complex for 50ns. The RMSD plot obtained from the simulation is attached here. The RMSD plot shows a stable trajectory for entire simulation,...

09 June 2024 7,886 1 View

Τ-Random Acceleration Molecular Dynamics (τ-RAMD) Simulation?

I want to calculate τ-Random Acceleration Molecular Dynamics (τ-RAMD) Simulation using NAMD/VMD software? Kindly provide input parameters that are essential to run these simulation. I will be very...

31 May 2024 2,662 2 View

Is anyone else investigating the formation of a two-phase system between a carbohydrate and a solvent?

Dear Experts, I am currently conducting a Molecular Dynamics (MD) simulation using the NAMD package to observe the formation of a two-phase system between glucose, acetonitrile, and water. To...

26 May 2024 5,711 2 View

How can we plot normalized density profile ρ(r)/ρ0 ?

Normalized density profile ρ(r)/ρ0 of metal ions around carbon nanotube from NAMD simulation data

20 May 2024 449 2 View

How merge output files of simulation with NAMD?

I have been running steered molecular simulation with NAMD, but in the middle of my simulation it has stopped and i have restarted from specific steps which had stopped. Finally i have two parts...

19 May 2024 1,483 2 View