From 9b8b7917e7065847c1eedddda61fd0cecc8b0ef3 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 21 Dec 2018 11:26:06 -0600
Subject: [PATCH] Made diffusivity vary with number of nucleotides represented
by bead
---
mrdna/segmentmodel.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/mrdna/segmentmodel.py b/mrdna/segmentmodel.py
index 1b9fb84..d4333ed 100644
--- a/mrdna/segmentmodel.py
+++ b/mrdna/segmentmodel.py
@@ -1963,6 +1963,8 @@ class SegmentModel(ArbdModel):
t.__dict__["nts"] = bead.num_nt*2 if char in ("D","O") else bead.num_nt
# t.name = t.name + "%03d" % (t.nts*10**decimals)
t.name = char + "%03d" % (beadtype_count[char])
+ t.mass = t.nts * 150
+ t.diffusivity = 150 if t.nts == 0 else min( 50 / np.sqrt(t.nts/5), 150)
beadtype_count[char] += 1
if self.DEBUG: print( "{} --> {} ({})".format(num_nt0, bead.num_nt, t.name) )
beadtype_s[key] = bead.type_ = t
--
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