Creating pull request to fix merge conflicts in my fork

README_E2EDNA.md → Module_Readme/README_E2EDNA.md

@@ -70,4 +70,4 @@ OpenDNA will repeat simulations of this length until either a predetermined maxi
 The two current conditions for calling off an MD run are:
 * The system has reached equilibrium, within a target thereshold. 
 Equilibration here is defined by the eigenvalue-weighted average slopes of the principal components of the 3D trajectory approaching zero, indicating either static behaviour or a sufficiently well-explored potential energy surface.
-* Unbinding: if OpenDNA detects that the analyte has detached from the aptamer and does not make contact for a preset amount of time (default = 1 nanosecond), the binding simulation will cut off, and the analyte-peptide pair are considered to be non-binding.
+* Unbinding: if OpenDNA detects that the analyte has detached from the aptamer and does not make contact for a preset amount of time (default = 1 nanosecond), the binding simulation will cut off, and the analyte-peptide pair are considered to be non-binding.

README_MDAnalysis.md → Module_Readme/README_MDAnalysis.md

@@ -9,4 +9,4 @@ We undertake a wide range of manipulations on this object, using mostly straight
 One point worth mentioning is on the functions for analysis of nucleic acids. 
 While there are preexisting functions for analysis e.g., of Watson-Crick hydrogen bond lengths in mda.analysis.nuclinfo, these functions are somewhat old, and prohibitively slow for analysis of lengthy trajectories.
 To remedy this, we have written the functions `getWCDistTraj` and `getNucDATraj` using modern, very fast MDA methods, for Watson-Crick hydrogen bond length and nucleic dihedral angle analysis respectively. 
-When we have time, we hope to clean these functions up for incorporation into MDA proper.
+When we have time, we hope to clean these functions up for incorporation into MDA proper.

README_MMB.md → Module_Readme/README_MMB.md

@@ -17,4 +17,4 @@ It is worth noting that MMB outputs, while technically valid 3D representations
 One may consider the raw MMB output as a 'coarse' or highly strained version of the 3D structure of the aptamer, which generally benefits from relaxation via MD simulation. 
 
 Finally, MMB output .pdb files are a bit quirky, and require post-processing to run properly in OpenMM. 
-See the comments in opendna.prepPDB for details.
+See the comments in opendna.prepPDB for details.

README_NUPACK.md → Module_Readme/README_NUPACK.md

@@ -12,4 +12,4 @@ A few key NUPACK features we take advantage of are:
 * Output explicit probability of observing the most likely secondary structure for a given sequence.
 * Output suboptimal structures and their probabilities for a given sequence.
 
-NUPACK has also a wealth of design and utility functions we encourage users to play with on their own.
+NUPACK has also a wealth of design and utility functions we encourage users to play with on their own.

README_OpenMM.md → Module_Readme/README_OpenMM.md

@@ -10,4 +10,4 @@ In the future, we hope to implement implicit solvation in OpenMM, which unfortun
 The OpenMM code itself is fairly self-explanatory, and we direct users to the excellent [documentation](http://docs.openmm.org/latest/userguide/index.html).
 
 One final point worth noting is that is is not clear whether the AMOEBA force field functional form implemented in OpenMM (corresponding the AMOEBA13) is fully compatible with e.g., the new nucleic acid parameters in AMOEBABIO18, even if one appropriately converts the TINKER .prm files to OpenMM .xml parameter files.
-For this reason, we advise users interested in AMOEBA simulations to look at our TINKER-based implementation of [E2EDNA](https://github.com/InfluenceFunctional/E2EDNA), which while less automated, is tailor-made for usage with AMOEBA.
+For this reason, we advise users interested in AMOEBA simulations to look at our TINKER-based implementation of [E2EDNA](https://github.com/InfluenceFunctional/E2EDNA), which while less automated, is tailor-made for usage with AMOEBA.