| Title | : | NAMD Tutorial #1 - Simulation of a Simple Protein |
| Duration | : | 16:41 |
| Viewed | : | 0 |
| Published | : | 04-05-2020 |
| Source | : | Youtube |
Thanks for watching! Contact me if you have any questions.
If you don't want to download TCL or the maxmin script, or simply want to run a quicker simulation without periodic boundary conditions:
1) Remove everything in between the equals sign borders (PME, Grouppressure, Langevinpiston)
2) Remove "CellBasisVector" 1, 2 and 3, remove "CellOrigin"
3) Change "WrapWater" and "WrapAll" to off
Download NAMD:
www.ks.uiuc.edu/Development/Download/download.cgi?…
CHARMM topologies and parameters:
mackerell.umaryland.edu/charmm_ff.shtml
Maxmin script:
m3g.iqm.unicamp.br/packmol/utilities.shtml
MAXMIN_NEW ADDITIONS:
puts " Cell centre: "
puts " X= [ expr ($xmax + $xmin)/2 ] "
puts " Y= [ expr ($ymax + $ymin)/2 ] "
puts " Z= [ expr ($zmax + $zmin)/2 ] "
puts "-------------------------------------------------------"
puts " Copy/paste for NAMD: "
puts "cellBasisVector1 [ expr $xmax - $xmin ] 0 0 "
puts "cellBasisVector2 0 [ expr $ymax - $ymin ] 0 "
puts "cellBasisVector3 0 0 [ expr $zmax - $zmin ] "
puts "cellOrigin [ expr ($xmax + $xmin)/2 ] [ expr ($ymax + $ymin)/2 ] [ expr ($zmax + $zmin)/2 ] "
puts "-------------------------------------------------------"
NAMD INPUT SCRIPT THAT I USED:
# ----------input-----
coordinates solvate.pdb
structure solvate.psf
parameters param.prm
paratypecharmm on
#bincoordinates minimized.restart.coor
#binvelocities minimized.restart.vel
# ----------output------
set output output
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50
binaryoutput yes
binaryrestart yes
outputEnergies 50
restartfreq 50
# ---------Basic dynamics-------
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
# --------Simulation space partitioning----
switching on
switchdist 9
cutoff 10
pairlistdist 11
# --------Multiple time stepping----
firsttimestep 0
timestep 2
stepspercycle 1
# -------Temperature control----
set temperature 310
temperature $temperature; # initial temperature
# -------Langevin Dynamics------
langevin on; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of 1/ps
langevinTemp $temperature; # bath temperature
# ===============================================
PME on
PMEGridSizeX 65
PMEGridSizeY 50
PMEGridSizeZ 55
# doesnt work with just pme
useGroupPressure yes
# with grouppressure, works better, holes still there
LangevinPiston on
LangevinPistonTarget 1.02
LangevinPistonPeriod 150
LangevinPistonDecay 90
LangevinPistonTemp $temperature
# with langevin piston, works!!! But slower.
# ===============================================
# Periodic Boundary conditions
cellBasisVector1 64.702 0 0
cellBasisVector2 0 49.82 0
cellBasisVector3 0 0 55.158
cellOrigin -5.7379999999999995 22.462999999999997 20.051000000000002
wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off
# ---------Scripting
minimize 100 ;# lower potential energy for 1000 steps
reinitvels $temperature ;# since minimization zeros velocities
run 50000;
# END
SHARE TO YOUR FRIENDS
Scan me
