AMBER Archive (2003) - May 2003 By Subject250 messages sorted by:
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Starting: Thu May 01 2003 - 10:46:05 CDT
Ending: Sat May 31 2003 - 11:44:46 CDT
- (no subject)
- 10-12 H-bond terms
- 2 questions
- A question about AMBER, leaprc.ff02EP
- a question about constructing a periodic box by PLEP.
- a question about scale factor
- A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations.
- A simple question about offset, want to make sure
- about the dielectric
- Amber 7.xx installation on FreeBSD
- Amber on SGI with Itanium compilers for linux
- Amber on SGI with Itanium compilers for linux (fwd)
- AMD opteron
- ANAL in AMBER
- anal, amber7 and resnum 0
- antechamber read gaussian file
- atomic positional fluctuation
- bad atom type f(fluorine) in MM-PBSA?
- best force field for Protein+DNA
- Calcium in proteins
- can not minimize
- center command
- CFP: Informatics Approaches in Structural Genomics at PSB 2004
- charge fitting for c-term homocysteine.
- clustering trajectories
- coordinate files from carnal
- current AMBER citation?
- difference between iwrap and image?
- distance-dependent dielectric function
- DNA base-step distortion
- Does Anyone Have a Working MACHINE File for Solaris/SPARC?
- Does Leap has a problem with Isoleucines?
- Etot is not constant in NVE ensemble
- EWALD BOMB
- Ewald: coeff, error estimate
- Fluorine atom type in mm_pbsa?
- force field parameters for torsions
- force field parameters for torsions (I am away)
- From Dr. Ekaterina Nikitina
- H-O-H angle
- HBOND energies in sander
- Heat of Vaporization
- help me switching from amber5 to amber6
- Help with Sander test output error
- how to set up a carbon nanotube pdb file
- Hybdrogen bonds and LJ 10-12
- I still have problems with parm99.dat
- Increase lastist in the &cntrl namelist
- information
- initial velocity
- IR6 and makeDIST-RST
- Latest Leap Compile Errors
- leap complains!
- LES analysis tool other than Moil-view
- Mainchain.dat
- MD input file for MM-PBSA calculations
- MD problem
- MD steps limit in sander (Amber 6)
- Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE
- minimizaiton in vacuum
- Minimization problem w/ counter-ion !
- minimization with restraints
- mm_gbsa question
- mm_pbsa and B/Z DNA relative stabilities
- mm_pbsa with PBCAL = 0
- multiple timesteps
- Newton-Raphson minimization for large systems
- no MD output
- non bonded pairlist?
- non-periodic system
- nucgen.dat
- off-diagonal VDW term
- Order parameters
- parameters for nitro group
- parm99
- Phosphorylated Serine Library
- Phosphotyrosine parametrization
- Pi-Pi stacking
- Please help on xleap: FATAL ERROR
- problem about virtual box?
- problem on MD simulation of damage DNA
- Problem with CMC/MD
- problems with anal in amber7
- protonate problem
- ptraj and rdf help
- ptraj generated PDB files
- ptraj rdf help
- Question about BELLY NMODE
- Questions about statistics output of mm_pbsa?
- Questoin about temperature
- Residual dipolar couplings
- RESP, constraining Dipole Moment
- RMSD fluctuation too much
- RMSF problem
- rotational and translational motion
- Sander help
- saveAmberParm problems in xleap
- serine/tyrosine in charged states
- Simple math of memory calculation for nmode
- Simple question about sander parameter set
- Simulation under physiological conditions
- SPC/E model -LJ parameters
- SPC/E water model
- translational and rotational motion (more information)
- unit of vlimit?
- upper limited of memory for nmode
- Use of Mg2+ in AMBER 7
- using distance restraints in Sander (AIX 4.3 RS6000)
- Using GLYCAM in sander with a non-zero 10-12 coefficient
- water box distortion
- water residence time analysis
- What kind of interactions are ignored for end group interactions
- Xleap adding torsions
- Xleap: 'triangular' and 'square' bond
Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:44 CDT
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