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PROTEIN FOLDING
Molecular Dynamics Simulation
ALL ATOM MODEL
GROMACS
BPTI constant pH_gromacs
1E0Q with gromacs
1E0Q REMD with GROMACS
NAMD
water_box_namd
Amber
SMD of 1E0Q
Water and Salt Solutions
create pure water box for Amber
TOP100 AMBER
Constant pH simulation of BPTI Implicit(amber)
Constant pH simulation of BPTI Explicit(Amber)
PH REPLICA EXCHANGE SIMULATION OF BPTI IMPLICIT_AMBER
PH REPLICA EXCHANGE SIMULATION OF BPTI EXPLICIT_AMBER
CHARMM & MMTSB
WATER SOLUTION_CHARMM
1E0Q with CHARMM GPU
constant pH simulation BPTI Implicit(charmm)
Constant pH Simulation BPTI Explicit(charmm)
Replica Exchange Simulation Introduction
REPLICA EXCHANGE SIMULATION
pH replica exchange simulation of BPTI implicit_charmm
Experiment of Rplica Exchange Simulation
Temperature REX Simulation of 1E0Q
MD simulation of BPTI
BPTI constant pH
Coarse Grained Models
GO Models in CHARMM
GO simulation in NAMD
Go REX simulation in MMTSB_1E0Q
GO_rex_BPTI
GO Martini model
MARTINI simulation of DPPC
Martini model of MORC16
Coarse Grained Lipids for Amber(CGLA)
Finding Water Bridges
LIPID
trans-2-aminocyclohexanol
Cyclohexane
MORC16
Catalog
100 proteins bechmark
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Search for:
Cyclohexane
The Cyclohexane Chair Flip – Energy Diagram
Substituted Cyclohexanes: “A Values”
Linux
VMD
TOOLSET
Water Bridge
HBONDS
WHAM
gnuplot
Gromacs
CHARMM and MMTSB tool set
Amber
NAMD
force field generation
CHARMM TOPOLOGY FILE
PH SIMULATION
Blocked Amino Acids
CHARMM
Resources
