From: sunyzero (sunyzero_at_163.com)
Date: Tue Dec 08 2015 - 22:00:19 CST
Hi Jerome,
Thank you very much, I will try it again, I hope I can find reasons.
sujun
At 2015-12-08 23:09:58, "Jérôme Hénin" <jerome.henin_at_ibpc.fr> wrote:
Hi "sunyzero",
How many degrees of freedom do you need to sample for your calculation to work?
Once you can answer that question, you'll have a much better idea how to proceed.
Jerome
On 8 December 2015 at 08:42, Souvik Sinha <souvik.sinha893_at_gmail.com> wrote:
I think increasing the sampling time will eventually decrease the barrier until convergence of sampling is achieved . And you can also use the "historyFreq " option to your restarin1.in file so that you can have the track for the pmf during the simulation.
On Tue, Dec 8, 2015 at 11:18 AM, sunyzero <sunyzero_at_163.com> wrote:
Dear Namd users
Hello, I need your help about determining the PMF with Adaptive Biasing Forces. According to tutorial about Methods for calculating Poteintials of Mean Force, I use it on HIV-1 protease inhibitors dissociation process,and inhibitors dissociate from binding site moving range from 0 to 36Å, which is divided into six window,each 6-Å wide,but in the ABF output .pmf file, the value of pmf is too large,the maximum value is 88kcal/mol. I try many times, there still exist questions.Here is one of my configures.
# 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
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 win1
restartfreq 500 ;# 1000steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500
colvars on
colvarsConfig restrain1.in
# Minimization
#minimize 500
#reinitvels $temperature
run 1500000 ;#
And here is my restrain1.in
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
name Translocation
width 0.1
lowerboundary 0.0
upperboundary 6.0
lowerwallconstant 100.0
upperwallconstant 100.0
distanceZ {
main {
atomnumbers { the atoms of ligand }
}
ref {
atomnumbers { the atoms of protein and name CA
}
}
axis ( 0.0, 0.0, 1.0 )
}
}
abf {
colvars Translocation
fullSamples 1000
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:38 CST