From: M. A (matabay2010_at_gmail.com)
Date: Fri May 28 2021 - 09:44:14 CDT
Hi J茅r么me,
Thank you for your reply . I understood but unfortunately I can not pay
and I need help. I prepared the extrabond files separately, but now I don't
know how to write the script in the config file to use these extrabond
files one after the other. If you can help me it would be kind of you. my
config file is:
# MD SETUP
timestep 2.0
##numsteps 1
# FLEXIBLE CELL
useflexiblecell no
# INPUT
structure ionized.psf
parameters par_all36_lipid.prm
parameters par_all36_prot.prm
parameters par_all22_prot.prm
parameters par_all27_prot_lipid_na.inp
parameters par_all36_cgenff.prm
parameters par_all36_na.prm
parameters par_all36_carb.prm
paraTypeCharmm on
coordinates ionized.pdb
bincoordinates equilibration.coor
binvelocities equilibration.vel
extendedsystem equilibration.xsc
# OUTPUT
outputenergies 500
outputtiming 500
outputpressure 500
binaryoutput yes
outputname forward
restartname forward
restartfreq 500
binaryrestart yes
XSTFreq 500
# DCD
DCDfreq 5000
DCDfile forward.dcd
# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSizeX 60
PMEGridSizeY 60
PMEGridSizeZ 110
# WRAP WATER FOR OUTPUT
wrapAll on
# CONSTANT-T
langevin on
langevinTemp 300.0
langevinDamping 1.0
# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 75
LangevinPistonDecay 25
LangevinPistonTemp 300
StrainRate 0.0 0.0 0.0
useGroupPressure yes
# SPACE PARTITIONING
splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 10
margin 1.0
# CUT-OFFS
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
limitDist 1.3
# RESPA
fullElectFrequency 2
nonbondedFreq 1
# 1-4 NON-BONDED
exclude scaled1-4
1-4scaling 1.0
# COM
commotion no
# SHAKE
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400
# COLVARS SECTION
extraBonds on
#extraBondsCosAngles off
extraBondsFile rest.pdb
# FEP PARAMETERS
source fep.tcl
alch on
alchType FEP
alchFile solvate.fep
alchCol B
alchOutFreq 2500
alchOutFile forward.fepout
alchElecLambdaStart 0.1
alchVdwLambdaEnd 1.0
alchVdwShiftCoeff 5.0
alchdecouple on
alchEquilSteps 5000
set numSteps 500000
set dLambda 0.0
runFEP 1.0 1.0 $dLambda $numSteps
best regards
Maryam
On Thu, May 27, 2021 at 1:58 PM J茅r么me H茅nin <jerome.henin_at_ibpc.fr> wrote:
> Dear Maryam,
>
> ----- On 27 Mai 21, at 9:30, M. A <matabay2010_at_gmail.com> wrote:
>
> Dear All,
>
> I am running MD simulation of ligand and protein interaction with the FEP
> method for calculation of free energy parameter. As is mentioned in page 36
> of the related tutorial (In silico alchemy: tutorial for alchemical
> free-energy perturbation calculations with NAMD), we can measure the
> free-energy cost incurred for fading out pseudo bonds by zeroing out
> reversibly the associated force constants, until the aforementioned
> contribution due to the loss of translational entropy be recovered. Does
> anybody know how we can decrease the value of K in the extrabond section of
> namd config file?
>
> The force constant is part of the extrabonds file. You will need a
> different extrabonds file for each value of the force constant. You can
> generate them with the scripting language of your choice. Then you need to
> run a NAMD simulation using each of the extrabonds files.
>
> I need the exact script
>
> How much are you willing to pay someone to do that for you?
>
>
> Best,
> J茅r么me
>
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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