FF2 name for E0LL2Y

Conflicts:

	django_simple/todo/jobfiles.py

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index c0b1667..e87cdcc 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -113,8 +113,8 @@ class TaskForm_min_a(forms.Form):
      name = forms.CharField(max_length=20)
 
      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
-                           label='Force Field',initial='E0LL2Y')
-     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
+                           label='Force Field',initial='FF2')
+#     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
      min_overlap = forms.BooleanField(required=False,label='remove overlap')
      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
@@ -230,7 +230,7 @@ class TaskForm_md_a(forms.Form):
      name = forms.CharField(max_length=20)
 
      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
-                           label='Force Field',initial='E0LL2Y')
+                           label='Force Field',initial='FF2')
      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
                       label='starting structure',initial='extconf')
      md_seq = forms.CharField(label='Sequence',
@@ -261,7 +261,7 @@ class TaskForm_md_a(forms.Form):
      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
                help_text='write trajectory every ntwe steps')
      md_dt = forms.FloatField(label='DT',initial=0.2,
-                  help_text='time step [mtu]')
+                  help_text='time step [mtu=48.9 fs]')
      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
                   help_text='coupling to the thermal bath (Berendsen)')
@@ -384,7 +384,7 @@ class TaskForm_remd_a(forms.Form):
      name = forms.CharField(max_length=20)
 
      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
-                           label='Force Field',initial='E0LL2Y')
+                           label='Force Field',initial='FF2')
      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
                       label='starting structure',initial='extconf')
      md_seq = forms.CharField(label='Sequence',
@@ -409,7 +409,7 @@ class TaskForm_remd_a(forms.Form):
      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
                help_text='write statfile every ntwe steps')
      md_dt = forms.FloatField(label='DT',initial=0.2,
-                  help_text='time step [mtu]')
+                  help_text='time step [mtu = 48.9 fs]')
      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
                   help_text='coupling to the thermal bath (Berendsen)')

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index e9a2ffc..e540b4c 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -84,7 +84,7 @@ def write_on_task_save(sender, instance, **kwargs):
 #wrapper = textwrap.TextWrapper(width=70)
 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
 
-     if  instance.unres_ff =='E0LL2Y':
+     if  instance.unres_ff =='FF2':
       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
@@ -295,7 +295,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
         
      if instance.type == 'min':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         shutil.copy('../files/pbs.csh','.')
       else:
         shutil.copy('../files/pbs_new.csh','pbs.csh')
@@ -303,7 +303,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir('..')
      elif instance.type == 'md':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs_md.csh', 'r')
       else:
         f1 = open('../files/pbs_md_new.csh', 'r') 
@@ -348,7 +348,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
         tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs8.csh', 'r')
       else:
         f1 = open('../files/pbs8_new.csh', 'r')

diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index ee54314..f5036ad 100644 (file)
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -9,7 +9,7 @@ import json
 MIN_CHOICE = (('minimize cart','minimize'),('minimize regular','regularize'),('minimize softreg','soft regularize'),('minimize','minimize internal coordinates'))
 MD_START= (('extconf','extended chain'),('pdbstart','start from pdb'),('rand_conf','random chain'))
 MD_LANG = (('langevin','Langevin'),('berendsen','Berendsen'))
-FF_CHOICE = (('E0LL2Y','JCC 30 2127 (2009) + JCTC 11 817831 (2015)'),('opt-wtfsa-2','JCIM 10.1021/acs.jcim.7b00254 (2017)'))
+FF_CHOICE = (('FF2','JCC 30 2127 (2009) + JCTC 11 817-831 (2015)'),('opt-wtfsa-2','JCIM 57 2364-2377 (2017)'))
 
 logger = logging.getLogger(__name__)
 
@@ -29,7 +29,7 @@ class Task(models.Model):
 #    def getssbond(self):
 #       return json.loads(self.ssbond)
 
-    unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='E0LL2Y')
+    unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='FF2')
     pdbcode = models.CharField(max_length=4,default='')
 # minimization
     min_choice = models.CharField(max_length=20,choices=MIN_CHOICE,default='minimize cart')

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 5909fae..262603f 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -459,7 +459,7 @@ def add_remd_a(request,task_id):
         form = TaskForm_remd_a(initial=data)     
      elif '_example_saxs' in request.POST:
         data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True,
-         'md_nstep':200000,'md_lang':'langevin','unres_ff':'E0LL2Y',
+         'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2',
          'remd_cluter_temp':270, 
          'scal_rad':4.0,'wsaxs':100.0,'saxs_data':
 """ 0.5     1.33868e-02
@@ -585,7 +585,7 @@ def addmlist(request,task_id):
              else:
               return redirect('/')
     else:
-      if task.unres_ff == 'E0LL2Y':
+      if task.unres_ff == 'FF2':
         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
         '["1", "1", "1", "1", "1", "1", "1", "1"]',
         'temperatures':