From: Cezary Czaplewski Date: Mon, 22 Jan 2018 15:46:15 +0000 (+0100) Subject: FF2 name for E0LL2Y X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=787a0b201a638f0a7ac7cec85d172bf0619f2fc1;p=django_unres.git 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 --- 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 --- 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 --- 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 --- 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':