From 9655895b90948062980e4889d6c23bbe2a1edb4b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sat, 9 Jul 2016 15:07:38 +0200
Subject: [PATCH] Resolve Bug... problems with Angstrom/Nanometer
---
modules/mol/mm/src/simulation.cc | 6 +++---
modules/mol/mm/src/system_creator.cc | 4 ++++
modules/mol/mm/src/topology.cc | 2 +-
3 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
index d4e411bec..570bbaf80 100644
--- a/modules/mol/mm/src/simulation.cc
+++ b/modules/mol/mm/src/simulation.cc
@@ -718,9 +718,9 @@ void Simulation::ResetHarmonicPositionRestraint(uint index, const geom::Vec3& re
int particle;
std::vector<double> parameters;
restraint_ptr->getParticleParameters(index,particle,parameters);
- parameters[0] = ref_position[0];
- parameters[1] = ref_position[1];
- parameters[2] = ref_position[2];
+ parameters[0] = ref_position[0] * 0.1;
+ parameters[1] = ref_position[1] * 0.1;
+ parameters[2] = ref_position[2] * 0.1;
parameters[3] = k;
parameters[4] = x_scale;
parameters[5] = y_scale;
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
index 223f7ea9e..aa365ee29 100644
--- a/modules/mol/mm/src/system_creator.cc
+++ b/modules/mol/mm/src/system_creator.cc
@@ -221,6 +221,10 @@ SystemPtr SystemCreator::Create(const TopologyPtr top,
j != i->second.end(); ++j){
parameters.push_back(*j);
}
+ parameters[0] *= 0.1;
+ parameters[1] *= 0.1;
+ parameters[2] *= 0.1;
+
position_restraint_force.addParticle(i->first[0], parameters);
}
}
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
index 819d2d500..58a72827d 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -1238,7 +1238,7 @@ void Topology::MergeTop(TopologyPtr other){
if(!harmonic_position_restraints.empty()){
for(std::vector<std::pair<Index<1>,std::vector<Real> > >::const_iterator i = harmonic_position_restraints.begin();
i != harmonic_position_restraints.end(); ++i){
- geom::Vec3 ref_pos(i->second[0],i->second[1],i->second[2]);
+ geom::Vec3 ref_pos(i->second[0], i->second[1], i->second[2]);
this->AddHarmonicPositionRestraint(old_num_particles + i->first[0],
ref_pos,
i->second[3],
--
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