From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Thu Sep 18 2008 - 13:33:07 CDT

Hello everyone,

I am having a problem with my sim that I can not seem to solve on my
own. I am simulating a protein resting just above a solid support
slab. The whole system is within a solvation box that is 5 Angs.
larger than the system in all dimensions. The solid support is
parallel to the xy-plane. I begin by running an min/equil totaling
100ps using the below config file then begin a npt sim using the other
script that I have copied below. My problem/observations are as
follows:

1) After running equil I transfer the .vel, .xsc, .psf, and .coor
files to another folder and use them to begin the npt sim.
2) When the sim is done I run it in VMD and have noticed that the
solid support is being tilted diagonally in the x-dimension (e.g. it
is no longer parallel to xy-plane as I initially set it up to be). It
seems to be being squeezed. This is a problem for what I am trying to
do.
3) When I took a look at the .xsc box size it is much smaller than
the xy-dimensions of the solid support. Thus, this leads me to
believe that this is at least part of the problem. But, of course, if
I increase the values of this extended system box my temp shoots up
quite a bit.
4) I have tried to run the sim with Flex on/off and with constant
area/ratio and none of these options change the outcome of the dreaded
tilited slab disease.
5) Can I change anything in the initial equil or system to change
this outcome?
6) Also, can anyone explain what the margin value represents and what
a margin of 5 vs. lets say 2 does to the outcome?

Thank you very much in advance.

Best,
Chris M Hartshorn
Washington State University
cmhartshorn_at_wsu.edu

SCRIPT #1-Min/Equil
#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# Protein & Slab with Water and ions

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

structure protein_slab_wations.psf
coordinates protein_slab_wations.pdb

set temperature 0
set outputname equil_out

firsttimestep 0

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

# Input parameters
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.0
switching on
switchdist 8.5
pairlistdist 11.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

# Periodic Boundary Conditions must be used when starting from scratch!!
cellBasisVector1 109.82 00.00 00.00
cellBasisVector2 00.00 105.35 00.00
cellBasisVector3 00.00 00.00 118.97
cellOrigin -0.0494995117 -0.09399986265 -2.80599975585

# An internal tuning parameter used in determining the size of the
cubes of
# space with which NAMD uses to partition the system
# The z dimension is going to shrink so pad sufficiently
margin 5

wrapWater on
wrapNearest off

# PME (for full-system periodic electrostatics) only with PBC's
# Must get cell dimensions from PBC basisvectors for accurate PME
# Remember multiples of 2,3, and/or 5
PME on
PMEGridSizeX 120
PMEGridSizeY 108
PMEGridSizeZ 120

# Constant Pressure Control (variable volume) only for PBC's
useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate independently
useConstantRatio no # constant shape in first two cell dimensions
useConstantArea yes # constant area and normal pressure
conditions

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 10 ;# damping coefficient (gamma) of 10/ps
langevinTemp 310
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Nos´e-Hoover Langevin piston pressure control
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp 310

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 100
xstFreq 100
outputEnergies 10
outputTiming 100
outputPressure 100
binaryoutput off

# Everything beyond this point is order dependent!!!!

#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Run one step to get into scripting mode
minimize 0

# Turn off until later
langevinPiston off

# Minimize all atoms
minimize 3000
output min_all

# Begin run with langevin on
run 5000
output heat

langevinPiston on
run 8000
output equil_ca

# equilibrate volume without restraints
# constraintScaling 0
run 84000

SCRIPT #2
#############################################################
## JOB DESCRIPTION ##
#############################################################

# 1000ps Molecular Dynamics run of
# Protein on Slab with Water

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

structure protein_slab_wations.psf
coordinates equil_out.coor
velocities equil_out.vel
extendedSystem equil_out.xsc
set temperature 310
set outputname nptsimFA_out

firsttimestep 100000

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

# Input parameters
# Temperature is not specified since initial velocities come
# from previous system using "velocities" option/file above
paraTypeCharmm on
parameters par_all27_prot_lipid_sil.inp

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.0
switching on
switchdist 8.5
pairlistdist 11.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
lighter damping than equilibration
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# When using a previous extendedSystem file it is not necessary to
define
# cellBasisVectors or cellOrigin because they are included in that
file!!!!!!

# An internal tuning parameter used in determining the size of the
cubes of
# space with which NAMD uses to partition the system
# The z dimension is going to shrink so pad sufficiently
margin 2

wrapWater on
wrapNearest off

# PME (for full-system periodic electrostatics) only with PBC's
# Must get cell dimensions from last frame of previous run for
accurate PME
# Remember multiples of 2,3, and/or 5
PME on
PMEGridSizeX 125
PMEGridSizeY 120
PMEGridSizeZ 100

# Constant Pressure Control (variable volume) only for PBC's
useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate independently
useConstantRatio no # constant shape in first two cell dimensions
useConstantArea yes # constant area and normal pressure
conditions

# Nos´e-Hoover Langevin piston pressure control
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 10
outputTiming 100
outputPressure 100
binaryoutput off

# Everything beyond this point is order dependent!!!!

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Constant N,T,P MD run
run 900000