<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thank you very much for writing! &nbsp;I have tried what was suggested, and the following errors were produced follow the use of the make mdrun command:<div><br></div><div><div>[100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o</div><div>Linking CXX executable mdrun-gpu</div><div>ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64)</div><div>Undefined symbols:</div><div>&nbsp;&nbsp;"OpenMM::Context::~Context()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_cleanup in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::getDefaultPluginsDirectory()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Context::getState(int) const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::MonteCarloBarostat::MonteCarloBarostat(double, double, int)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::getNonbondedMethod() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Context::setVelocities(std::vector&lt;OpenMM::Vec3, std::allocator&lt;OpenMM::Vec3&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::CustomTorsionForce::CustomTorsionForce(std::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::getCutoffDistance() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::setCutoffDistance(double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::getPlatform(int)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::addException(int, int, double, double, double, bool)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::AndersenThermostat::AndersenThermostat(double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::setPropertyDefaultValue(std::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;, std::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::HarmonicBondForce::addBond(int, int, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getPotentialEnergy() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::GBSAOBCForce::setNonbondedMethod(OpenMM::GBSAOBCForce::NonbondedMethod)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::CustomTorsionForce::addPerTorsionParameter(std::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::VerletIntegrator::VerletIntegrator(double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::getPropertyNames()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::NonbondedForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::GBSAOBCForce::GBSAOBCForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::setEwaldErrorTolerance(double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::CustomTorsionForce::addTorsion(int, int, int, int, std::vector&lt;double, std::allocator&lt;double&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::System::System()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::getNumPlatforms()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::PeriodicTorsionForce::PeriodicTorsionForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::GBSAOBCForce::addParticle(double, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getKineticEnergy() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::System::~System()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_cleanup in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Context::getPlatform()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::PeriodicTorsionForce::addTorsion(int, int, int, int, int, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getTime() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::addParticle(double, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::HarmonicBondForce::HarmonicBondForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getVelocities() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Context::setPositions(std::vector&lt;OpenMM::Vec3, std::allocator&lt;OpenMM::Vec3&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::CMMotionRemover::CMMotionRemover(int)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::BrownianIntegrator::BrownianIntegrator(double, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Platform::loadPluginsFromDirectory(std::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::HarmonicAngleForce::HarmonicAngleForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::GBSAOBCForce::setCutoffDistance(double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::System::addConstraint(int, int, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::System::setDefaultPeriodicBoxVectors(OpenMM::Vec3 const&amp;, OpenMM::Vec3 const&amp;, OpenMM::Vec3 const&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::RBTorsionForce::RBTorsionForce()", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::NonbondedForce::setNonbondedMethod(OpenMM::NonbondedForce::NonbondedMethod)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::HarmonicAngleForce::addAngle(int, int, int, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::LangevinIntegrator::LangevinIntegrator(double, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getForces() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::Context::Context(OpenMM::System&amp;, OpenMM::Integrator&amp;, OpenMM::Platform&amp;)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::State::getPositions() const", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_copy_state in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp;"OpenMM::RBTorsionForce::addTorsion(int, int, int, int, double, double, double, double, double, double)", referenced from:</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>&nbsp;&nbsp; &nbsp; &nbsp;_openmm_init in libopenmm_api_wrapper.a(openmm_wrapper.cpp.o)</div><div>ld: symbol(s) not found</div><div>collect2: ld returned 1 exit status</div><div>make[3]: *** [src/kernel/mdrun-gpu] Error 1</div><div>make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2</div><div>make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2</div><div>make: *** [mdrun] Error 2</div><div><br></div><div>I did use the OpenMM software provided on their website for Mac. &nbsp;Is there a workaround for this issue?</div><div><br></div><div>Thanks again for the help!</div><div><br></div><div>Best,</div><div><br></div><div>Solomon Berman</div><div>Department of Chemistry</div><div>Boston University</div><div><br></div><div><div>On Nov 15, 2010, at 5:44 PM, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(127, 127, 127); "><b>From:<span class="Apple-converted-space">&nbsp;</span></b></span><span style="font-family: Helvetica; font-size: medium; ">Rossen Apostolov &lt;<a href="mailto:rossen@kth.se">rossen@kth.se</a>&gt;<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(127, 127, 127); "><b>Date:<span class="Apple-converted-space">&nbsp;</span></b></span><span style="font-family: Helvetica; font-size: medium; ">November 15, 2010 5:13:06 PM EST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(127, 127, 127); "><b>To:<span class="Apple-converted-space">&nbsp;</span></b></span><span style="font-family: Helvetica; font-size: medium; "><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(127, 127, 127); "><b>Subject:<span class="Apple-converted-space">&nbsp;</span></b></span><span style="font-family: Helvetica; font-size: medium; "><b>Re: [gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span style="font-family: Helvetica; font-size: medium; color: rgb(127, 127, 127); "><b>Reply-To:<span class="Apple-converted-space">&nbsp;</span></b></span><span style="font-family: Helvetica; font-size: medium; ">Discussion list for GROMACS users &lt;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br></span></div><br><br>Hi,<br><br>Did you run CMake in a fresh directory? If not try<br><br>$ rm CMakeCache.txt<br>$ cmake -DGMX_OPENMM=ON<br>$ make mdrun<br><br>Cheers,<br>Rossen<br><br>On 11/14/10 5:58 PM, Solomon Berman wrote:<br><blockquote type="cite">Good day friends,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am trying to install mdrun-gpu on my MacBook Pro, using Mac OS X Snow Leopard v. 10.6.5.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I typed the following commands into the terminal screen while in the gromacs-4.5.3 source directory.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cmake -DGMX_OPENMM=ON<br></blockquote><blockquote type="cite">make mdrun<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The following error messages are produced:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">[ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o<br></blockquote><blockquote type="cite">/gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’:<br></blockquote><blockquote type="cite">/gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)<br></blockquote><blockquote type="cite">/gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: (Each undeclared identifier is reported only once<br></blockquote><blockquote type="cite">/gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: for each function it appears in.)<br></blockquote><blockquote type="cite">/gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)<br></blockquote><blockquote type="cite">make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1<br></blockquote><blockquote type="cite">make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2<br></blockquote><blockquote type="cite">make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2<br></blockquote><blockquote type="cite">make: *** [mdrun] Error 2<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am not sure how to troubleshoot these error messages. &nbsp;I know this is a new implementation, where we were originally given precompiled binaries for download, so this may or may not be unique to the switch over.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any help anyone would be willing to provide, I would be greatly appreciative. Thank you!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Solomon Berman<br></blockquote><blockquote type="cite">Department of Chemistry<br></blockquote><blockquote type="cite">Boston University--<br></blockquote><blockquote type="cite">gmx-users mailing list &nbsp;&nbsp;&nbsp;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at<span class="Apple-converted-space">&nbsp;</span><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a><span class="Apple-converted-space">&nbsp;</span>before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to<span class="Apple-converted-space">&nbsp;</span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read<span class="Apple-converted-space">&nbsp;</span><a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></blockquote></blockquote></div><br></div></body></html>