Fix restart simulation for GaWTM-eABF

fhh2626 · Apr 29, 2023 · c2b7859 · c2b7859
1 parent 2ce5860
commit c2b7859
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Showing 3 changed files with 22 additions and 10 deletions.
diff --git a/BFEE2/gui.py b/BFEE2/gui.py
@@ -1667,10 +1667,7 @@ def f():
                         QMessageBox.warning(self, 'Error', 
                                 f'\
 The feature of using GaWTM-eABF as the workhorse engine is \
-experimental! Known issues:\n \
-The config files for extending GaWTM-eABF simulations \
-will do pre-equilibration again. This may cause some errors. \
-One can revise the config file manually to avoid it'
+experimental! Please always use the latest devel version of NAMD!\n'
                         )
 
                     try:

diff --git a/BFEE2/templates_namd/configTemplate.py b/BFEE2/templates_namd/configTemplate.py
@@ -189,8 +189,8 @@ def namdConfigTemplate(
                 configString += f'\
 colvarsConfig    {cvFile}                       \n'
 
-            if CVRestartFile != '':
-                configString += f'\
+                if CVRestartFile != '':
+                    configString += f'\
 colvarsInput     {CVRestartFile}                \n'
 
 
@@ -211,13 +211,16 @@ def namdConfigTemplate(
                 configString += f'\
 accelMD                         on                     \n\
 accelMDG                        on                     \n\
+accelMDdihe                     on                     \n\
+accelMDOutFreq                  1000                   \n\
+accelMDGSigma0D                 6.0                    \n'
+                if CVRestartFile == '':
+                     # new GaMD-WTM-eABF simulation
+                     configString += f'\
 accelMDGcMDSteps                500000                 \n\
 accelMDGcMDPrepSteps            100000                 \n\
 accelMDGEquiPrepSteps           100000                 \n\
 accelMDGEquiSteps               500000                 \n\
-accelMDdihe                     on                     \n\
-accelMDOutFreq                  1000                   \n\
-accelMDGSigma0D                 6.0                    \n\
 for {{set stage 0}} {{$stage < 2}} {{incr stage}} {{   \n\
     if {{$stage == 0}} {{                              \n\
         puts "Probing the GaMD parameters..."          \n\
@@ -230,6 +233,18 @@ def namdConfigTemplate(
         run norepeat   {numSteps}                      \n\
     }}                                                 \n\
 }}                                                     \n'
+                else:
+                     configString += f'\
+accelMDGcMDSteps                0                      \n\
+accelMDGcMDPrepSteps            0                      \n\
+accelMDGEquiPrepSteps           0                      \n\
+accelMDGEquiSteps               0                      \n\
+accelMDGRestart                 on                     \n\
+accelMDGRestartFile             {CVRestartFile}.gamd   \n\
+colvarsConfig                   {cvFile + ".amd"}      \n\
+colvarsInput                    {CVRestartFile}        \n\
+run norepeat   {numSteps}                              \n'
+
         else:
             # currently the alchemical route is somewhat hard-coded
             # this will be improved in the future

diff --git a/unitTest/userDefinedPath.py b/unitTest/userDefinedPath.py
@@ -1,2 +1,2 @@
-VMDPATH = r'C:/Program Files/VMD/vmd.exe'
+VMDPATH = r'D:/Program Files (x86)/University of Illinois/VMD/vmd.exe'
 UNITTESTPATH = r'D:/Users/fhh26/Documents/GitHub/BFEE2/unitTest'