From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Oct 06 2017 - 17:35:33 CDT
Hi Rabeta,
Are you sure they restrained the protein? Normally I see these z-restraints on the lipids so that the lipids don't drift to the top or bottom of the simulation box and cause discontinuities in the collective variable when they are rewrapped to the other side of the periodic boundary, although I guess restraining the protein would have the same effect. Basically those extra restraints are there so that they can have "wrapAll on". If you only wrapped water, and did not include water in your collective variable (or don't wrap at all), you don't need the restraints.
-Josh
On 10/06/2017 04:19 PM, Rabeta Yeasmin wrote:
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<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdynamicsgmail.google.com&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C75f49d1e42004faf5a4208d50d08530c%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636429251776233735&sdata=c9e60apOvLKQY%2B%2Fv2B8nsEaZvJmu6%2FaiFHoegXFmA%2B4%3D&reserved=0>
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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