From: juan du (dujuan709_at_gmail.com)
Date: Wed Nov 24 2010 - 08:00:49 CST
> Hi, everyone
> I am continuing NAMD equilibration runs using restart files. I give
> the last step of previous run as the firsttimestep for the new run.
> Some terms are different from each other. What's more, I calculated
> the RMSD of the backbone atoms using the initial structure as
> reference. The RMSD values increase significantly after each restart.
> I wonder if there is something wrong with the restart. Any help would
> be appreciated.
>
> Juan Du
>
> Last step
> ENERGY: 250000 43292.9642 29263.0362 3945.3575
> 441.5854 -506610.3555 47059.5022 1164.0174
> 0.0000 117463.1912 -263980.7016 311.2331 -381443.8928
> -262914.2342 309.6929 -239.3309 -267.4445
> 1220176.8696 17.9805 19.0874
>
> new run first step
> ENERGY: 0 43292.9642 29263.0362 3945.3575
> 441.5854 -506613.0293 47061.8423 0.0000
> 0.0000 117462.0335 -265146.2102 311.2300 -382608.2437
> -264084.8769 311.2300 186.2934 158.2625
> 1220172.1958 186.2934 158.2625
>
> Laststep
> # NAMD extended system configuration output file
> 250000 106.858 0 0 0 106.858 0 0 0 106.858 0.037 0.054 -0.008
> 2.27649e-05 2.27649e-05 2.27649e-05 0 0 0
>
> new run first
> # NAMD extended system trajectory file
> 0 106.858 0 0 0 106.858 0 0 0 106.858 0.037 0.054 -0.008 2.27649e-05
> 2.27649e-05 2.27649e-05 0 0 0
> .conf file
>
> #set temperature 310.0
> set targetemp 310.0
> set coorfile ../hv57-334.pdb
> set laststep myeqrst1
>
> #--Input File
> coordinates $coorfile
> structure ../hv57-334.psf
> bincoordinates ${laststep}.coor
> binvelocities ${laststep}.vel
> extendedSystem ${laststep}.xsc
>
> #--Output File
> outputname myeqout2
> restartname myeqrst2
> outputEnergies 100
> binaryoutput yes
> xstFreq 1000
> DCDFreq 1000
> restartFreq 1000
>
> #--Initialization
> COMmotion no
> timestep 1 ;# 2fs/step
> #rigidBonds all ;# needed for 2fs/step
> nonbondedFreq 1
> fullElectFrequency 2
>
> #--Temperature ReScaling
> rescaleFreq 100
> #rescaleTemp $temperature
> rescaleTemp $targetemp
>
> #--Constant T
> langevin on
> langevinDamping 1.
> langevinTemp $targetemp
> langevinHydrogen off ;# do not couple bath to hydrogens
>
> #--Constant P
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
> useConstantRatio no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar --> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $targetemp
>
> #--PME
> PME on
> PMETolerance 0.000001
> PMEGridSpacing 1.0
>
> #--Constraint
> constraints on
> consexp 2
> consref $coorfile
> conskfile ../prot-fix2.cnst ;# force constant value
> conskcol B
> constraintScaling 20.0 ;# the FC is 20 kcal/mol Angstrom
> margin 10
>
> #--parameter file
> paraTypeCharmm on
> parameters ../par_all27_prot_lipid.prm
>
> exclude scaled1-4
> 1-4scaling 1.0
> dielectric 1.0
> switching on
> switchdist 10.0
> cutoff 12.0
> pairlistdist 14.0 ;# cutoff + 2
> stepspercycle 10 ;# follow NAMD configuration file
>
> wrapWater on
> wrapAll on
>
> #--simulation time
> run 250000
>
>
> RMSD
> mol new hv57-334.pdb
> mol new hv57-334.psf type psf first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
> mol addfile myeqout1.dcd type dcd first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
> mol addfile myeqout2.dcd type dcd first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
> proc print_rmsd_through_time {} {
> set outfile [open rmsd.dat w]
> set reference [atomselect 0 "protein and backbone"]
> set compare [atomselect 1 "protein and backbone"]
> set num_steps [molinfo 1 get numframes]
>
> for {set frame 0} {$frame < $num_steps} {incr frame} {
> $compare frame $frame
> set trans_mat [measure fit $compare $reference]
> $compare move $trans_mat
> set rmsd [measure rmsd $compare $reference]
> puts $outfile "RMSD of $frame is $rmsd"
> }
> }
>
> print_rmsd_through_time
>
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