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How to run a simulation in 15 steps
* Create a clean directory in your home directory. This is where you put all the files needed. * Copy . . . NAMD output files will be written. * Create a NAMD equilibration script. * Create the NAMD.sh submission . . .
3K - last updated 2004-11-18 14:35 UTC by P.S. Georgoulia

Molecular Dynamics studies of the (Ala2-Leu2)8
* [[Project description]] * [[Progress reports]] * [[NAMD minimisation and heating-up script]] * [[NAMD . . .
1K - last updated 2005-04-24 12:41 UTC by glykos

NAMD equilibration script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel . . .
2K - last updated 2004-11-16 16:16 UTC by georgoulia

Running a molecular dynamics simulation of native Rop
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . ** cd ../equi ** *mkdir output* * Create a NAMD equilibration script with the name /equi.namd/ . . .
27K - last updated 2005-09-27 12:03 UTC by server.cluster.mbg.gr

Running a molecular dynamics simulation of protein G in a hexagonal cell
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . ** cd ../equi ** *mkdir output* * Create a NAMD equilibration script with the name /equi.namd/ . . .
25K - last updated 2005-09-27 12:05 UTC by server.cluster.mbg.gr

Running a molecular dynamics simulation of the Dickerson (DNA) dodecamer
What follows is a mostly complete description of the /practical/ steps required for performing a short . . . ** cd ../equi ** *mkdir output* * Create a NAMD equilibration script with the name /equi.namd/ . . .
30K - last updated 2005-09-27 12:04 UTC by server.cluster.mbg.gr

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