Questions tagged [gromacs]
GROMACS software package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Primarily designed for biochemical molecules like proteins, lipids and nucleic acids.
8
questions with no upvoted or accepted answers
6
votes
0
answers
94
views
Calculating bending modulus of a CG model of a surface from MD simulation
I have built a CG (Martini) model of a 2D Nanomaterial. For now, I want to calculate its bending rigidity. As far as I know, the bending modulus can be computed by making the nanomaterial infinite - i....
- 1,066
5
votes
0
answers
69
views
Loading Gromacs Trajectories using ASE (Atomic-Silumation-Environment)
I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to ...
- 969
4
votes
0
answers
39
views
MMGBSA: Electrostatic and van der Waals
I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
- 41
4
votes
0
answers
44
views
Quantifying binding free energy?
I have binding free energy of some organic molecules on a surface, computed through Umbrella sampling. For now, I only have experimental data on the binding energy of some of these molecules. Is it ...
- 1,066
4
votes
0
answers
91
views
Density of a spherical droplet of water on top of graphene
I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
- 1,066
4
votes
0
answers
29
views
Three point bending test on a 2D nanomaterial with SMD in gromacs
I want to see the bending response of my 2D nanomaterial, where the force is applied at the midpoint of the sheet using SMD (constant-velocity). Here, I have kept the two ends fixed. So, I want to ...
- 1,066
3
votes
0
answers
28
views
CHARMM36 Parameters for Neutral Arginine
I am looking for CHARMM36 parameters for Neutral Arginine. Protonated form of Argnine is already available in CHARMM36 library, but not the same for Neutral. Thanks.
With best regards
- 1,066
2
votes
0
answers
30
views
Error Simulating bulk diemthyl-ether with angle constrain in gromacs
I am trying to simulate bulk dimethyl ether with total constraints, both bonds and angles.
I am using lincs with constraint = all-angles in *.mdp file in gromacs.
I am attaching the error I ...
- 121