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Apply constraints to desire molecules
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0
|
2
|
March 25, 2025
|
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Dynamic POSRES_FC assignment in .mdp
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8
|
27
|
March 24, 2025
|
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LINCS error while performing pull simulations?
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17
|
57
|
March 18, 2025
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Assistance with Fixing a Spherical Structure in Umbrella Sampling
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0
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15
|
March 17, 2025
|
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Cutoff-dependent deviations in free energy for force switching and potential shifting
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19
|
148
|
March 17, 2025
|
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Lambdas in FEP calculations
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3
|
1173
|
March 7, 2025
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Direct continuation of pulling after changing mdp parameters
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1
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10
|
March 4, 2025
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Is it necessary to apply external pressure in the deformation direction?
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6
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45
|
March 4, 2025
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[MD Simulation Error] Fatal PME Rank Issue: Particles Moving Out of Domain Decomposition Cell
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2
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20
|
March 4, 2025
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Change in position of Histidine residue lead to difference in columb interaction energy
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0
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4
|
March 3, 2025
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Mdp parameters : pull-coord1-geometry = distance vs direction
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0
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14
|
March 3, 2025
|
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How to perform the oscillatory shear by gromacs?
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0
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10
|
February 27, 2025
|
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Setting up Environment and Obtaining .tpr files
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4
|
28
|
February 26, 2025
|
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CGENFF not working
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0
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16
|
February 24, 2025
|
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Issue with direction-periodic and periodicity during umbrella sampling
|
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4
|
26
|
February 17, 2025
|
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Handling D-Amino Acids in MDP File for GROMACS Simulations
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2
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15
|
February 15, 2025
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Free energy difference is zero for non-zero coulomb-lambdas during solvation free energy calculation
|
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3
|
22
|
February 13, 2025
|
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Different temperautres for gen-temp and tocupl
|
|
2
|
14
|
February 13, 2025
|
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Segmentation fault in MARTINI 2.2 with pulling
|
|
16
|
50
|
February 12, 2025
|
|
Position restraints for Umbrella sampling simulation of membrane protein-ligand
|
|
6
|
219
|
February 11, 2025
|
|
Pull simulations giving LINCS error
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|
1
|
19
|
February 11, 2025
|
|
Pressure application to separate oil in water through amorphous polymer membrane
|
|
14
|
66
|
February 8, 2025
|
|
H-bond constraint
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|
4
|
2063
|
February 6, 2025
|
|
Unfolding a 574 aa protein
|
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0
|
31
|
February 3, 2025
|
|
CHARMM force field parameters for Ru(II)
|
|
0
|
39
|
January 29, 2025
|
|
Simulating pulling a small solute across a lipid bilayer
|
|
7
|
29
|
January 28, 2025
|
|
Brownian Dynamics (friction coefficient vs tau_t)
|
|
1
|
28
|
January 28, 2025
|
|
NPT steps warnings
|
|
0
|
38
|
January 22, 2025
|
|
Continuation in mdp file for umbrella sampling
|
|
2
|
32
|
January 21, 2025
|
|
Constraints Option with Flat-Bottom Position Restraints in mdp file
|
|
2
|
20
|
January 20, 2025
|