From: Lutimba Stuart (lutimba.stuart_at_scilifelab.se)
Date: Wed Feb 21 2018 - 13:49:36 CST
Dear all
When running targeted MD simulations of a substrate entering into a
membrane protein binding pocket the substrate reaches its final destination
in a few ns although the total simulation time is 100ns, The issue is that
the RMSD distance does not evolve linearly in the specified time.
MY other issue is the continuation of from the last step when running TMD,
to make a total of 100ns, and to easily queue in my jobs at the cluster, i
have been creating dependencies but the sugar reaches its binding pocket in
the first 4 ns so on continuation from the last step in order to make
100ns, NAMD just runs the ordinary equilibration since the sugar is already
at the binding site, Am not sure if am running this in the right way, Am
grateful for any assistance and attached please is the configuration file
that am using.
####################################################################
set infile lac-TMD06
set outfile lac-TMD07
timestep 1.0
numsteps 10000000
structure occl_E325+H.psf
paraTypeCharmm on
parameters toppar_water_ions.str
parameters par_all36_prot.prm
parameters par_all36_lipid.prm
parameters par_all27_prot_lipid.prm
parameters par_all36_carb.prm
coordinates occl_E325+H.pdb
bincoordinates ${infile}.coor
binvelocities ${infile}.vel
outputname ${outfile}
outputEnergies 10000
outputTiming 10000
#outputPressure 100
#minimization on
stepspercycle 20
rigidBonds all
fullElectFrequency 4
nonbondedFreq 2
exclude scaled1-4
1-4scaling 1.0
switching on
vdwForceSwitching yes
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
#set temperature 310
#temperature $temperature
extendedSystem ${infile}.xsc
#cellBasisVector1 105 0.0 0.0
#cellBasisVector2 0.0 108 0.0
#cellBasisVector3 0.0 0.0 85
cellOrigin -0.02 0.02 0.03
restartname ${outfile}
restartfreq 10000
DCDfile ${outfile}.dcd
DCDfreq 10000
DCDUnitCell yes
XSTfile ${outfile}.xst
XSTfreq 10000
PME on
PMEGridSizeX 140
PMEGridSizeY 140
PMEGridSizeZ 90
#99 on protein
#constraints off
#consref LacYO-POPE-restraint-2.pdb
#conskfile LacYO-POPE-restraint-2.pdb
#conskcol B
#heave bgal fixe
#fixedatoms on
#fixedatomsfile LacY+H-o-pose-1.ref
#fixedatomscol B
#fixedatomsforces on
langevin on
langevinDamping 5
langevinTemp 310
useGroupPressure yes #must be used with rigigBonds (shake)
useFlexibleCell yes #box dimension can fluctuate
LangevinPiston on #use Langevin piston pressure control
LangevinPistonTarget 1.0 #pressure in bar
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 310
TMD on
TMDk 7 #Elestic constant (kcal/mol/Å)
TMDOutputFreq 1000
TMDFile Lac-occl+H+TMD.pdb
TMDFirstStep 0
TMDLastStep 10000000
#TMDInitialRMSD 0
TMDFinalRMSD 0
#TMDDiffRMSD off
#TMDFile2
############################################################
#####################
Lutimba Stuart
Masters Student
Skovde University Sweden
Science for Life Laboratory (Scilife) Sweden
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