MBG wiki: Search for: equilibration script

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Create the files needed
*What is needed: **A force field parameter file **A force field topology file **A pdb file with the initial . . . the files referred as heating-up script and equilibration script **A psf file which contains structural . . .
2K - last updated 2004-10-11 09:26 UTC by server.cluster.mbg.gr

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 . . . 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-Ile2)6
*[[Project Description]] *[[Progress Reports]] *[[NAMD Ala2Ile2 minimization and heating-up script]] . . . *[[NAMD Ala2Ile2 equilibration script]] *[[NAMD Ala2Ile2 restart script]] . . .
1K - last updated 2004-11-19 12:32 UTC by C.I. Papaioannou

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

NAMD Ala2Ile2 equilibration script
<source> # # Input files # structure ionized.psf coordinates heat_out.coor velocities heat_out.vel . . .
2K - last updated 2004-11-16 16:21 UTC by server.cluster.mbg.gr

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/ containing . . .
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/ containing . . .
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/ containing . . .
30K - last updated 2005-09-27 12:04 UTC by server.cluster.mbg.gr

equilibration NAMD script for T40W
*[[equilibration script]] *[[restart1 script]] *[[restart2 script]] . . .
1K - last updated 2004-10-03 12:52 UTC by natasa.biology.uoc.gr

equilibration script
<source> structure ionized.psf coordinates heat_out.coor velocities heat_out.vel extendedSystem . . .
1K - last updated 2004-10-12 11:24 UTC by server.cluster.mbg.gr

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