|
Dear all, This .mdp file below is from an old tutorial. How would it look in the new version?
|
|
2
|
28
|
April 30, 2025
|
|
Lincs Warning-Alchemical free energy calculations
|
|
0
|
16
|
April 24, 2025
|
|
+++ assertion failed: i>0 serial of an atom cannot be zero
|
|
3
|
21
|
April 23, 2025
|
|
CGENFF not working
|
|
1
|
34
|
April 20, 2025
|
|
Topology for janus MoSSe
|
|
0
|
5
|
April 14, 2025
|
|
Cutoff-dependent deviations in free energy for force switching and potential shifting
|
|
23
|
191
|
April 10, 2025
|
|
1 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decompo
|
|
0
|
8
|
April 9, 2025
|
|
AWH Error During Ligand-Membrane Pulling in Z-direction
|
|
1
|
27
|
April 4, 2025
|
|
Is the frame interval important for studying the membrane properties?
|
|
1
|
8
|
April 3, 2025
|
|
Converting HMMM solvent parameters for GROMACS
|
|
0
|
13
|
March 31, 2025
|
|
Issue with GROMACS Simulation : MDP file parameters and NVT equilibration
|
|
4
|
38
|
March 31, 2025
|
|
Apply constraints to desire molecules
|
|
3
|
27
|
March 28, 2025
|
|
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance' Replacing old mdp entry '
|
|
1
|
14
|
March 28, 2025
|
|
Dynamic POSRES_FC assignment in .mdp
|
|
8
|
36
|
March 24, 2025
|
|
LINCS error while performing pull simulations?
|
|
17
|
67
|
March 18, 2025
|
|
Assistance with Fixing a Spherical Structure in Umbrella Sampling
|
|
0
|
15
|
March 17, 2025
|
|
Lambdas in FEP calculations
|
|
3
|
1205
|
March 7, 2025
|
|
Direct continuation of pulling after changing mdp parameters
|
|
1
|
14
|
March 4, 2025
|
|
Is it necessary to apply external pressure in the deformation direction?
|
|
6
|
53
|
March 4, 2025
|
|
[MD Simulation Error] Fatal PME Rank Issue: Particles Moving Out of Domain Decomposition Cell
|
|
2
|
29
|
March 4, 2025
|
|
Change in position of Histidine residue lead to difference in columb interaction energy
|
|
0
|
4
|
March 3, 2025
|
|
Mdp parameters : pull-coord1-geometry = distance vs direction
|
|
0
|
16
|
March 3, 2025
|
|
How to perform the oscillatory shear by gromacs?
|
|
0
|
15
|
February 27, 2025
|
|
Setting up Environment and Obtaining .tpr files
|
|
4
|
32
|
February 26, 2025
|
|
Issue with direction-periodic and periodicity during umbrella sampling
|
|
4
|
43
|
February 17, 2025
|
|
Handling D-Amino Acids in MDP File for GROMACS Simulations
|
|
2
|
16
|
February 15, 2025
|
|
Free energy difference is zero for non-zero coulomb-lambdas during solvation free energy calculation
|
|
3
|
31
|
February 13, 2025
|
|
Different temperautres for gen-temp and tocupl
|
|
2
|
16
|
February 13, 2025
|
|
Segmentation fault in MARTINI 2.2 with pulling
|
|
16
|
54
|
February 12, 2025
|
|
Position restraints for Umbrella sampling simulation of membrane protein-ligand
|
|
6
|
245
|
February 11, 2025
|