Sample umbrella sampling input file

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Oct 06 2017 - 17:14:02 CDT

Dear NAMD users,

I am trying to do umbrella sampling to find pmf during trans passing of a
protein through a lipid bilayer. I restrained the distance of COM of lipid
and protein using colvar file. But when I checked the sample input file of
umbrella sampling in NAMD forum, It looks like they have restrained z
coordinate of some of the atoms of protein along with restraining the COM
distance of the ammonia and protein. I am wondering if only restraining the
distance in the colvar file is not enough. I have out the sample input file
for umbrella sampling below and highlighted the portion I am confused-

Thanks very much.

Rabeta Yeasmin

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

# ABF of NH3 in AmtB, window 1

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

structure ../../../example-input/AmtB-system.psf
coordinates ../../../example-input/AmtB-system.pdb

binCoordinates ../../../example-input/AmtB-${num}.restart.coor
extendedSystem ../../../example-input/AmtB-${num}.restart.xsc

set temperature 310
set outputname win${num}A

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters ../../par_all27_prot_lipid_cmap.inp
parameters ../../toppar_amines.str
temperature $temperature

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

# Integrator Parameters
timestep 1.0 ;# 2fs/step (only if needed to finish quickly)
rigidBonds water ;# needed for 2fs steps
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Constant Temperature Control
langevin on ;# do langevin dynamicsgmail.google.com
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
#cellBasisVector1 70.2 0. 0.
#cellBasisVector2 0. 69.3 0.
#cellBasisVector3 0. 0 95.0
#cellOrigin -8.83 -7.92 -5.34

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
useGroupPressure no ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

constraints on
consexp 2
consref ../../../example-input/rest6.ref
conskfile ../../../example-input/rest6.ref
conskcol O
selectConstraints on
selectConstrX off
selectConstrY off
selectConstrZ on

colvars on
colvarsConfig US-win${num}.in

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

# Minimization
#minimize 500
#reinitvels $temperature

run 6000000 ;#

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