abrupt deviation in rmsd values

From: Monika Sharma (mon_sharma_at_research.iiit.ac.in)
Date: Wed May 02 2007 - 10:35:38 CDT

Dear All,
I am new to this MD thing and newer to NAMD. I am trying to unfolding
simulation of a small protein. And the protocol I am using is like:

   1. Energy minimization with fixed atoms, then with no fixed atoms
   2. Heating the system form 0 to 480 k using Langevin Dynamics
   3. Position restratined MD, fixing backbone atoms, and then
   4. free MD equilibration.

The run ends ok, but when i plot the rmsd over time. the plot shows the
deviation of about 4.0 in the initial phase of 10 ps or so... :-(
When I look at the log file created, its seen that the temperature rises
abruptly from 0 to 167K in a first go; whereas I have given it the incr
of 48K with each run. Dont know where the problem arises. May be the
sudden increase of the temp is destabilizing the protien to such an
extent. Can there be other possible way for getting the temperature
increased gradually?? I am attaching the .conf file and the rmsd data
file for the reference. If anybody can help me out.

----------------------------------------------------------------------------------------------------------------------
the execution code is like..
#Minimization

#run to get into scripting mode
minimize 0

# turn off pressure control
langevinPiston off
#minimize non-backbone atoms
minimize 2500

#minimize all atoms
fixedAtoms off
minimize 2500

#Heat with Ps restrained
for {set temp 0} {$temp <= 480} {incr temp 48} {
    run 10000
}
#equilibrate volume with Ps restrained
langevinPiston on
run 100000
#equilibrate volume without restraints
constraintScaling 0
run 500000
------------------------------------------------------------------------------------------------------------------------------


#molecules
set import ionized
set minim runmod_incr
set export run_270407
structure ${import}.psf
coordinates ${import}.pdb
bincoordinates ${minim}.coor
extendedSystem ${minim}.xsc

#forcefield parameters
paratypecharmm on
parameters /home/guest/projects/c32b1/toppar/par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0

#integrator parameters
timestep 1.0
fullElectFrequency 4

outputenergies 100
outputTiming 100
outputPressure 100
#initial config
set init_temp 0
set desired_temp 480
temperature $init_temp

#outputfiles and restart options
outputname ${export}
binaryoutput no
restartname run_270407_res
restartfreq 1000
binaryrestart yes
dcdfreq 1000
xstfreq 1000

#others
nonbondedFreq 1
rigidBonds all
rigidTolerance 1.00E-7
stepspercycle 20

#simulation spacing partitioning
switching on
switchDist 10
cutoff 12
pairlistdist 16
margin 1

#Periodic Boundary Conditions
cellBasisVector1 38 0 0
cellBasisVector2 0 41 0
cellBasisVector3 0 0 45
cellOrigin 4 -4 -16

wrapWater on
wrapAll on
wrapNearest on

#PME params
PME yes
PMEGridSpacing 1.0
PMEGridSizeX 45
PMEGridSizeY 45
PMEGridSizeZ 45

#Fixed atoms for initial heating up steps
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile zwv_fix_backbone.pdb
fixedAtomsCol B

#Restrained atoms for initial heating-up
constraints on
consRef zwv_constraint_ca.pdb
consKFile zwv_constraint_ca.pdb
consKCol B

#langevin dynamics params

#langevin temp control
Langevin on
LangevinDamping 4
LangevinHydrogen on
LangevinTemp $desired_temp
#langevin pressure control
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $desired_temp
useGroupPressure yes

#Minimization

#run 1 step to get into scripting mode
minimize 0

#turn off pressure control until later
langevinPiston off
#minimize non-backbone atoms
minimize 2500

#minimize all atoms
fixedAtoms off
minimize 2500

#Heat with Ps restrained
for {set temp 0} {$temp<=480} {incr temp 48} {
 run 10000
}

#equilibrate volume with Ps restrained
langevinPiston on
run 100000
#equilibrate volume without restraints
constraintScaling 0
run 500000


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