User littleworth

17 votes

3 answers

3k views

What does ns/day mean in high-performance computing?

asked Oct 29, 2021 at 8:12

13 votes

3 answers

4k views

What does "force field" mean?

asked Nov 3, 2021 at 2:16

11 votes

2 answers

1k views

How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

asked Dec 25, 2021 at 11:53

10 votes

3 answers

2k views

How to perform "gmx make_ndx" with single command line bypassing the interactive shell?

asked Dec 28, 2021 at 6:14

10 votes

2 answers

1k views

Molecular dynamics frame distorted by VMD?

asked Dec 21, 2021 at 3:13

10 votes

2 answers

3k views

How to calculate the computational time required for a MD simulation

asked Oct 31, 2021 at 4:56

9 votes

2 answers

539 views

How to simulate peptide solubility using molecular dynamics (GROMACS)?

asked Dec 29, 2021 at 13:34

9 votes

1 answer

1k views

How to manage disk space for Gromacs XTC (trajectory) file output

asked Dec 23, 2021 at 8:40

8 votes

1 answer

228 views

How to assign "Trajectory Smoothing Window Size" inside VMD Tcl script

asked Dec 30, 2021 at 5:32

8 votes

1 answer

482 views

Alternative to CGenFF for generating large ligand topology

asked Dec 21, 2021 at 7:52

7 votes

0 answers

147 views

How to determine minimum reasonable MD timing for ligand-protein complex [closed]

asked Dec 18, 2021 at 12:57

7 votes

1 answer

553 views

How to create molecule image similar with molconvert using RDKit

asked Oct 27, 2021 at 23:56

6 votes

2 answers

1k views

How to initiate protein-ligand docking with MD simulation tools

asked Oct 30, 2021 at 0:52

6 votes

1 answer

2k views

How to show electrostatic interactions in Pymol or other on the wanted residue

asked Oct 30, 2021 at 23:06

6 votes

1 answer

1k views

How to visualize protein-ligand complex MD run using VMD

asked Dec 20, 2021 at 8:52

6 votes

2 answers

2k views

How to show orientation axis in Pymol

asked Jun 23, 2022 at 12:48

5 votes

1 answer

493 views

Why are ligands restrained when simulating a protein-ligand complex with MD?

asked Dec 24, 2021 at 14:35

4 votes

1 answer

179 views

What is the curve fitting model used for the "Qubit™ Protein Assay Kit"?

asked May 24, 2022 at 11:54

4 votes

2 answers

358 views

How to orient the protein for lipid bilayer simulation in Gromacs

asked Sep 26, 2022 at 5:19

3 votes

0 answers

365 views

How to fix outliers in Ramachandran plot using Coot [closed]

asked Jul 15, 2022 at 11:38

2 votes

1 answer

134 views

How to control the thickness of lipid bilayer with GROMACS

asked Sep 27, 2022 at 3:37

Stack Exchange Network

21 Questions

What does ns/day mean in high-performance computing?

What does "force field" mean?

How to choose appropriate energy term in GROMACS MD simulation (Lennard-Jones or Coulomb)?

How to perform "gmx make_ndx" with single command line bypassing the interactive shell?

Molecular dynamics frame distorted by VMD?

How to calculate the computational time required for a MD simulation

How to simulate peptide solubility using molecular dynamics (GROMACS)?

How to manage disk space for Gromacs XTC (trajectory) file output

How to assign "Trajectory Smoothing Window Size" inside VMD Tcl script

Alternative to CGenFF for generating large ligand topology

How to determine minimum reasonable MD timing for ligand-protein complex [closed]

How to create molecule image similar with molconvert using RDKit

How to initiate protein-ligand docking with MD simulation tools

How to show electrostatic interactions in Pymol or other on the wanted residue

How to visualize protein-ligand complex MD run using VMD

How to show orientation axis in Pymol

Why are ligands restrained when simulating a protein-ligand complex with MD?

What is the curve fitting model used for the "Qubit™ Protein Assay Kit"?

How to orient the protein for lipid bilayer simulation in Gromacs

How to fix outliers in Ramachandran plot using Coot [closed]

How to control the thickness of lipid bilayer with GROMACS