Merge pull request #65 from fhh2626/dev

merge dev branch
fhh2626 · Jun 11, 2021 · 9a3391b · 9a3391b
2 parents bb81a18 + fd5c82a
commit 9a3391b
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Showing 4 changed files with 11 additions and 8 deletions.
diff --git a/BFEE2/gui.py b/BFEE2/gui.py
@@ -194,7 +194,7 @@ def _initUI(self):
         self.nonStandardSolvent.setLayout(self.nonStandardSolventLayout)
 
         # stratification
-        self.stratification = QGroupBox('Stratification windows')
+        self.stratification = QGroupBox('Stratification (number of strata)')
         self.stratificationLayout = QGridLayout()
 
         self.stratificationRMSDBoundLabel = QLabel('RMSD(Bound):')
@@ -240,7 +240,7 @@ def _initUI(self):
         self.pinDownProCheckbox = QCheckBox('Pinning down the protein')
         self.pinDownProCheckbox.setChecked(True)
 
-        self.useOldCvCheckbox = QCheckBox('Use custom-function-based CVs')
+        self.useOldCvCheckbox = QCheckBox('Use quaternion-based CVs')
         self.useOldCvCheckbox.setChecked(True)
 
         self.compatibilityLayout.addWidget(self.pinDownProCheckbox)
@@ -335,7 +335,7 @@ def _initUI(self):
         self.mainLayout = QVBoxLayout()
 
         # stratification windows
-        self.stratification = QGroupBox('Stratification windows')
+        self.stratification = QGroupBox('Stratification (number of strata)')
         self.stratificationLayout = QGridLayout()
 
         self.boundLigandLabel = QLabel('Ligand/Bound state:')
@@ -359,10 +359,10 @@ def _initUI(self):
         self.stratification.setLayout(self.stratificationLayout)
 
         # double-wide simulation
-        self.doubleWide = QGroupBox('Double-wide simulation')
+        self.doubleWide = QGroupBox('Double-wide sampling simulation')
         self.doubleWideLayout = QGridLayout()
 
-        self.doubleWideCheckbox = QCheckBox('Generate input files for double-wide simulations')
+        self.doubleWideCheckbox = QCheckBox('Generate input files for double-wide sampling')
         self.doubleWideCheckbox.setChecked(False)
         self.doubleWideLayout.addWidget(self.doubleWideCheckbox)
         self.doubleWide.setLayout(self.doubleWideLayout)
@@ -383,7 +383,7 @@ def _initUI(self):
         self.pinDownProCheckbox = QCheckBox('Pinning down the protein')
         self.pinDownProCheckbox.setChecked(True)
 
-        self.useOldCvCheckbox = QCheckBox('Use custom-function-based CVs')
+        self.useOldCvCheckbox = QCheckBox('Use quaternion-based CVs')
         self.useOldCvCheckbox.setChecked(True)
 
         self.compatibilityLayout.addWidget(self.pinDownProCheckbox)

diff --git a/BFEE2/templates_namd/configTemplate.py b/BFEE2/templates_namd/configTemplate.py
@@ -140,7 +140,7 @@ def namdConfigTemplate(
 wrapWater            on                         \n\
 langevin             on                         \n\
 langevinDamping      1                          \n\
-langevinTemp         300                        \n\
+langevinTemp         {temperature}              \n\
 langevinHydrogen     no                         \n\
 langevinpiston       on                         \n\
 langevinpistontarget 1.01325                    \n\

diff --git a/BFEE2/templates_namd/scriptTemplate.py b/BFEE2/templates_namd/scriptTemplate.py
@@ -62,6 +62,9 @@
 mol new ${path}.psf
 mol addfile ${path}.pdb
 set aa [atomselect top all]
+$$aa set beta 0
+set solute [atomselect top "not water and not ion"]
+$$solute set beta 1
 $$aa writexyz ${path}.xyz
 ${extraCommand}
 exit

diff --git a/BFEE2/version.py b/BFEE2/version.py
@@ -1 +1 @@
-__VERSION__ = '2.1.10'
+__VERSION__ = '2.1.11'