updated version info and improved DNA example. (The version info chan…

…ges reflects the bugfix in the previous commit. The "dsDNA_2beads=3bp" example was modified to improve efficiency.)

examples/coarse_grained/DNA_models/dsDNA/2strands/dsDNA_2beads=3bp_2019-10-19/moltemplate_files/dna_forcefield.lt

@@ -8,10 +8,9 @@ DNAForceField {
   # Choosing the particle masses:
 
   write_once("Data Masses") {
-    @atom:A          17097.9497
-    @atom:B          17097.9497
+    @atom:A          2553.29
+    @atom:B          2553.29
   }
-
   # Why?  Molecular motion at small length scales is Brownian (not ballistic).
   # Consequently, particle masses do not matter.  We can choose the
   # them to be anything we like as long as the physical processes we are
@@ -21,15 +20,15 @@ DNAForceField {
   # stable.  This makes it much easier to combine radically different kinds
   # of coarse-grained molecules together in the same simulation later on.
   # For numerical stability, all oscillations in the simulation should not
-  # occur faster than once every 30 timesteps.  Let's define Nperiod=30.
+  # occur faster than once every 12 timesteps.  Let's define Nperiod=12.
   # The mass, m, is determined by assuming that the timestep width, Δt=1, and
   #    sqrt(k_max/m) = 2π/(Nperiod*Δt)    and solving for m
   # --> m = (k_max*(Nperiod**2)/((2*pi)**2))
   # (For harmonic forces, k is the largest spring constant. More generally
   # k_max should be an upper bound for the second derivative of the energy with
   # respect to position, d^2U(r)/dr^2, which is accessible at this temperature.
   # This depends on the force-field you are using and the temperature.
-  #    In this case: I set k_max ≈ 750 kcal/mol / nm^2 (when temperature≈300K).
+  #    In this case: I set k_max ≈ 650 kcal/mol / nm^2 (when temperature≈300K).
   # Here there are 2 types of particles in this DNA backbone: "A" and "B".
   # They correspond to the DNA backbone for the two opposite chains.  I gave
   # them different atom type names to make it easy to distinguish them visually
@@ -343,7 +342,7 @@ DNAForceField {
     # For the dihedral angle (φb), during ITERATION 0, we assume that:
     #        Probability(φb) ≈ exp(-U(φb) / kB*T)    where:
     #        U(φb) = C3*(1 - cos(φb-φb0))*sin(θ1)*sin(θ2)
-    #             ≈ C3*(1/2)(φb-φb0)^2
+    #              ≈ C3*(1/2)(φb-φb0)^2
     # From the PDB files, the observed distribution of φb angles is:
     #        Probability(θ) ≈ exp(-σ*(1/2)*(φb-μ)^2)   where
     # equating the two expressions for Probability(φb)  (converting deg->rad)

examples/coarse_grained/DNA_models/dsDNA/2strands/virus_dsDNA_2beads=3bp_2019-10-19/moltemplate_files/dna_forcefield.lt

@@ -8,10 +8,9 @@ DNAForceField {
   # Choosing the particle masses:
 
   write_once("Data Masses") {
-    @atom:A          17097.9497
-    @atom:B          17097.9497
+    @atom:A          2553.29
+    @atom:B          2553.29
   }
-
   # Why?  Molecular motion at small length scales is Brownian (not ballistic).
   # Consequently, particle masses do not matter.  We can choose the
   # them to be anything we like as long as the physical processes we are
@@ -21,15 +20,15 @@ DNAForceField {
   # stable.  This makes it much easier to combine radically different kinds
   # of coarse-grained molecules together in the same simulation later on.
   # For numerical stability, all oscillations in the simulation should not
-  # occur faster than once every 30 timesteps.  Let's define Nperiod=30.
+  # occur faster than once every 12 timesteps.  Let's define Nperiod=12.
   # The mass, m, is determined by assuming that the timestep width, Δt=1, and
   #    sqrt(k_max/m) = 2π/(Nperiod*Δt)    and solving for m
   # --> m = (k_max*(Nperiod**2)/((2*pi)**2))
   # (For harmonic forces, k is the largest spring constant. More generally
   # k_max should be an upper bound for the second derivative of the energy with
   # respect to position, d^2U(r)/dr^2, which is accessible at this temperature.
   # This depends on the force-field you are using and the temperature.
-  #    In this case: I set k_max ≈ 750 kcal/mol / nm^2 (when temperature≈300K).
+  #    In this case: I set k_max ≈ 650 kcal/mol / nm^2 (when temperature≈300K).
   # Here there are 2 types of particles in this DNA backbone: "A" and "B".
   # They correspond to the DNA backbone for the two opposite chains.  I gave
   # them different atom type names to make it easy to distinguish them visually
@@ -343,7 +342,7 @@ DNAForceField {
     # For the dihedral angle (φb), during ITERATION 0, we assume that:
     #        Probability(φb) ≈ exp(-U(φb) / kB*T)    where:
     #        U(φb) = C3*(1 - cos(φb-φb0))*sin(θ1)*sin(θ2)
-    #             ≈ C3*(1/2)(φb-φb0)^2
+    #              ≈ C3*(1/2)(φb-φb0)^2
     # From the PDB files, the observed distribution of φb angles is:
     #        Probability(θ) ≈ exp(-σ*(1/2)*(φb-μ)^2)   where
     # equating the two expressions for Probability(φb)  (converting deg->rad)

moltemplate/scripts/moltemplate.sh

@@ -6,8 +6,8 @@
 # Copyright (c) 2013
 
 G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="2.17.5"
-G_DATE="2020-4-11"
+G_VERSION="2.17.6"
+G_DATE="2020-4-18"
 
 echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
 echo "" >&2

setup.py

@@ -45,9 +45,9 @@
 
   url='https://github.com/jewettaij/moltemplate',
 
-  download_url='https://github.com/jewettaij/moltemplate/archive/v2.17.5.zip',
+  download_url='https://github.com/jewettaij/moltemplate/archive/v2.17.6.zip',
 
-  version='2.17.5',
+  version='2.17.6',
 
   keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
             'ESPResSo'],