Amber Archive Dec 2020 by subject
- [AMBER] ABMD NFE queries
- [AMBER] amber 20 compilation problem
- [AMBER] amber 20 compilation problem (David A Case)
- [AMBER] Amber 4/pre Amber 7 binaries?
- [AMBER] AMBER Digest, Vol 3215, Issue 1
- [AMBER] Amber20 Installation Error
- [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2?
- [AMBER] ambpdb or other scipt?
- [AMBER] An error during NPT/production (GPU run)
- [AMBER] Antechamber vs R.E.D. Server
- [AMBER] app.run_mmpbsa() and mdout files were not created
- [AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem
- [AMBER] Box info not found in prmtop file
- [AMBER] box_dims question
- [AMBER] Bug AmberTools20 parallel installation
- [AMBER] C++ Programmer Position
- [AMBER] Calculation halted while running simulation
- [AMBER] Cannot minimize structure with sander
- [AMBER] Cation-pi interaction characterization
- [AMBER] cellulose crystal structure ( cellulose bundles)
- [AMBER] Charged species with antechamber
- [AMBER] CMP-GMP
- [AMBER] Conversion .rst to .inpcrd
- [AMBER] Cpptraj (post-processing rotation)
- [AMBER] cpptraj warnings topology flags being ignored
- [AMBER] CPU versus GPU Divergent Minimizations
- [AMBER] cremer
- [AMBER] crystallographic plane
- [AMBER] Disulphide bonds
- [AMBER] doubt frames simulation
- [AMBER] Effects of scalpha in softcore runs
- [AMBER] Electrostatic distance plot
- [AMBER] error after simulation
- [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20
- [AMBER] Error in Quasi-Harmonic Entropy
- [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20
- [AMBER] ff15ipq-m force field for protein mimetics
- [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card
- [AMBER] G quadruplex ions minimization
- [AMBER] Getting error while compile AMBER20 with cuda support
- [AMBER] Has anyone tried and succeeded at compiling Amber 18 with CUDA 11?
- [AMBER] how to convert (psf) to (prmtop) and (incprd)
- [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps
- [AMBER] how to know degrees of system
- [AMBER] How to proceed if system charge is non-zero and non-integral
- [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file
- [AMBER] How to use GAFF2?
- [AMBER] Hydrogen bond and Dissociation constant
- [AMBER] Identifying the equilibrated production region of a MD simulation trajectory
- [AMBER] Imaging issue in DNA - cpptraj
- [AMBER] lj1264 in vacuum
- [AMBER] MD run on GPU machine
- [AMBER] Minimization Time Limit Error with Sander
- [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme
- [AMBER] Mixing Force Constants In DISANG Files
- [AMBER] MMBSA.py.MPI installation
- [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20
- [AMBER] MMPBSA.py bad atom type: M1 error
- [AMBER] MMPBSA.py.MPI installation
- [AMBER] MMPBSA.py.MPI not build in Amber20
- [AMBER] MMPBSA.py.MPI parallel installation using run_cmake
- [AMBER] Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber
- [AMBER] nc files contain lesser number of atoms compared to prmtop
- [AMBER] Negative values in RDF analyses?
- [AMBER] NOE analysis with cpptraj
- [AMBER] parameters for benzene, pyerene, anthracene, and coronene
- [AMBER] Parmed error
- [AMBER] pbsa calcerror
- [AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory
- [AMBER] Position of the solute (center of mass) in the simulation box
- [AMBER] positive Amber FF energies?
- [AMBER] Problem forming circular DNA
- [AMBER] PROTEIN-DNA rmsd plot
- [AMBER] Query on some old sander inputs (dele, idiel, dielc)
- [AMBER] Question about atomic charges
- [AMBER] question about dihedral angles
- [AMBER] question pmemd.cuda
- [AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies
- [AMBER] Regarding Gaussian Accelerated MD
- [AMBER] Regarding Ions renumbering.
- [AMBER] Regarding to the parameters setup in SMD simulation
- [AMBER] Renumbering
- [AMBER] Reweighting error in Gaussian accelerated MD- PyReweighting-1D.py
- [AMBER] RMSD Protein-DNA complex Plot
- [AMBER] S2 order parameter not being calculated in IRED analysis.
- [AMBER] SHAKE problem
- [AMBER] Stacking distance in CPPTRAJ
- [AMBER] strange jump in the rmsd protein complex
- [AMBER] Terminal O5'/O3' for nucleosides in ff86?
- [AMBER] TI electrostatic free energy
- [AMBER] TI electrostatic free energy]
- [AMBER] tleap building a peptide
- [AMBER] tleap seems Si atom as S ... I don't know why
- [AMBER] Top Mode Contribution in PCA Analysis.
- [AMBER] Tri-coordination environment in zinc
- [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA
- [AMBER] Using sander.MPI in Docker
- [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating
- [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
- Last message date: Thu Dec 31 2020 - 19:00:02 PST
- Archived on: Wed Dec 04 2024 - 05:56:01 PST