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,
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',
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)')
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',
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)')
#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 &
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')
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')
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')
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__)
# 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')
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
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':