Commit dbaaef73 authored by cmaffeo2's avatar cmaffeo2
Browse files

Unscaled bases are now fixed during initial minimization, should be more robust

parent 62412139
......@@ -33,6 +33,7 @@ class CanonicalNucleotide():
for k1,k2 in zip(('name','type'),('f1','f2')):
self.props[k1] = [str(x,'utf-8') for x in d[k2]]
self.props['beta'] = np.ones(len(d['f1']))
# self.props['name'] = [str(x) for x in d['f1']]
# self.props['type'] = [str(x) for x in d['f2']]
......@@ -82,6 +83,7 @@ class CanonicalNucleotide():
rvec = scale*(rvec-r0) + r0
for k,r in zip(('x','y','z'), rvec):
c.props[k][i] = r
c.props["beta"][i] = 0
else:
if self.sequence in ("A","G"):
i0 = self.index("N9")-1
......@@ -94,6 +96,7 @@ class CanonicalNucleotide():
rvec = scale*(rvec-r0) + r0
for k,r in zip(('x','y','z'), rvec):
c.props[k][i] = r
c.props["beta"][i] = 0
return c
......
......@@ -1409,7 +1409,14 @@ cellBasisVector3 0 0 1000
if {$nLast == 0} {
temperature 300
minimize 4800
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile $prefix.pdb
fixedAtomsCol B
minimize 2400
fixedAtoms off
minimize 2400
} else {
bincoordinates output/$prefix-$nLast.restart.coor
binvelocities output/$prefix-$nLast.restart.vel
......
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