From: Sujata Roy (sujataroy1_at_gmail.com)
Date: Tue Dec 23 2014 - 05:41:12 CST

Dear all,
I am facing a problems during MD simulation. My system is a protein small
molecule complex, dimension was after heating for 100ps was
104,90 and 96 (x,y and z direction) then in equilibration I simulated the
system in constant pressure (The script is pasted below). After 900ps
simulation we found the box size is reduced (90,65,104). We also analysed
the rmsd of the system and we found steep raise of rmsd after heating to
equi state(0.77 to 2.41). But ideally the rmsd should increase smoothly.
Please help me. I should mention here that I simulated the system in
equilibrium state in a constant temperature, that time we found big bubble
inside the waterbox, so we simulated the system to reach equi state in
constant pressure.
sujata

*********************************************************************************************************************************************

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# COMMENT ON YOUR SYSTEM HERE

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure /homenc/eribi04/sujatarec/3DJY/3DJYdocki.psf
coordinates
 /homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_min3.pdb

set temperature 300
set outputname /homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_equi

#firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters
 /homenc/eribi04/sujatarec/4NOS/par_all27_prot_na_curcux.prm
#you may need to specify a path
#temperature 300

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Restart options Continuing a job from the restart files

#################################################
binCoordinates
 /homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_heat.restart.coor
extendedSystem
 /homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_heat.restart.xsc
binVelocities
 /homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_heat.restart.vel

set xscfile
/homenc/eribi04/sujatarec/3DJY/djy-dyna/3DJYdocki_heat.restart.xsc
#########################################################
proc get_first_ts { xscfile } {
   set fd [open $xscfile r]
   gets $fd
   gets $fd
   gets $fd line
   set ts [lindex $line 0]
   close $fd
   return $ts
}
set firstts [get_first_ts $xscfile]
########################################################
firsttimestep $firstts

# Constant Temperature Control
#langevin on ;# do langevin dynamics
#langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
#langevinTemp $temperature
#langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100

#############################################################
## PBC PARAMETERS ##
#############################################################

# Periodic Boundary Conditions
cellBasisVector1 78.26 0.0 0.0
cellBasisVector2 0.0 40.04 0.0
cellBasisVector3 0.0 0.0 90.56
cellOrigin 32.15 -20.31 -25.20

wrapWater on
wrapAll on
PME yes
PMEGridSizeX 73
PMEGridSizeY 78
PMEGridSizeZ 89
#############

#############
#fixed
#############
#fixedAtoms on
#fixedAtomsFile D:/curcumin/fixpro.pdb
#fixedAtomsCol B

# Constant Temperature Control
#langevin on ;# do langevin dynamics
#langevinDamping 5 ;# damping coefficient (gamma) of5/ps
#langevinTemp $temperature
#langevinHydrogen off ;# don't couple langevin bath to #hydrogens

# Constant Pressure Control
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp $temperature
######################################################
run 450000
********************************************************************************************************************************************