Amber Archive Dec 2004 by subject
- AMBER:
- AMBER: (no subject)
- AMBER: 1-4 EEL
- AMBER: a question
- AMBER: About MM/PBSA, PB Calculation
- AMBER: amber7 on digital unix
- AMBER: Binding free energy from separate/single trajectory
- AMBER: calculate ligand's rmsd
- AMBER: cluster analysis with ptraj in amber 8.0
- AMBER: cobalt parameters
- AMBER: Compiling Antechamber/Amber8 with ia64_ifort
- AMBER: Compiling question
- AMBER: constraints on atoms
- AMBER: converting from NAMD trajectory format
- AMBER: cut-off & MD
- AMBER: Dielectric Constant
- AMBER: Dummy Atoms: How to create them?
- AMBER: Dummy torsion paramters for thermodynamic integration
- AMBER: energy unit
- AMBER: entropy implementation in ptraj
- AMBER: Ewald
- AMBER: extracting energy from trajector?
- AMBER: FEP along a reaction coordinate in sander
- AMBER: Free Energy Perturbation using Sander (TI Method)
- AMBER: General Question about AMBER's Free Energy Perturbation Method
- AMBER: Gigabit Ethernet Switch/Opteron 246
- AMBER: How is optimization done during energy minimization of the force field?
- AMBER: how to prepare Zn.lib
- AMBER: Ideal bonds and angles
- AMBER: imin=5 in sander
- AMBER: Implicit 4r md
- AMBER: Implicit Solvent Models
- AMBER: increasing the maximum value of NPHB parameter
- AMBER: input conversion error [Amber8]
- AMBER: install problem
- AMBER: Kinetics energy
- AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem)
- AMBER: MD simulations on heparin and heparin sulfate
- AMBER: md's
- AMBER: MD: Water network analysis + visualization
- AMBER: mm_gbsa results for charged ligands
- AMBER: mm_pbsa
- AMBER: mm_pbsa +fillratio
- AMBER: MM_PBSA calculation error
- AMBER: MM_PBSA calculations
- AMBER: Molecular modelling.
- AMBER: nanotube parameters
- AMBER: nmode & mm-pbsa
- AMBER: nmode problem
- AMBER: NMR constraint problem
- AMBER: No radius found for 2412 Zn Zn
- AMBER: nrespa=2
- AMBER: NSCM
- AMBER: ntt parameter
- AMBER: one question about dielectric dependent model
- AMBER: Output of sander
- AMBER: parameter development
- AMBER: pbsa error in mm_pbsa amber 8
- AMBER: Problem with computing Resp charges using RED
- AMBER: ptraj hbond memory allocation on opteron
- AMBER: question about md's
- AMBER: question about MGB and PB
- AMBER: question about mmpbsa
- AMBER: question about parallel simulation
- AMBER: Question concerning ANAL total energy calculation
- AMBER: Question on tleap of amber8
- AMBER: Residue Loading Problem
- AMBER: restrainted torsion
- AMBER: RMSD of ligand
- AMBER: sander imin=5
- AMBER: Sander TI
- AMBER: some questions....
- AMBER: strange bond energies
- AMBER: SUSE 9.1 and AMBER 8
- AMBER: TFE parameters
- AMBER: unknown elements
- AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules
- AMBER: Why the charge is not an integer?
- AMBER: Why the surface calculations sometimes fail?
- AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation
- two processor amd 64 bit pc
- Last message date: Fri Dec 31 2004 - 17:53:00 PST
- Archived on: Wed Dec 25 2024 - 05:53:25 PST
