From: Christine Horejs (horejs_at_gmx.net)
Date: Fri Apr 20 2007 - 07:19:12 CDT
Hi everybody!
The .dat file of my abf simulation for a pmf calculation is zero for every xi-step and I can't find the mistake in my configuration file!
I want to calculate the pmf for a large molecule, when it is unfolded.
Can anybody help me? PLease!
Here is the configuration file and the .dat file:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Sphere
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure sbsb.psf
coordinates sbsb.pdb
set temperature 300
set outputname sbsb_pmf
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 2.95680737495 38.6497306824 40.4132194519
sphericalBCr1 107.0
sphericalBCk1 10
sphericalBCexp1 2
source /hpc_home/rtscheli/NAMD/NAMD_2.6_Linux-amd64/lib/abf/abf.tcl
package require abf
abf coordinate distance
abf abf1 5
abf abf2 13742
abf dxi 0.01
abf xiMin 108.0
abf xiMax 118.0
abf outFile sbsb.dat
abf fullSamples 500
#abf inFiles {}
abf distFile sbsb.dist
abf forceconst 20.0
abf dSmooth 0.0
abf applyBias yes
abf historyFile sbsb.history
abf writeXiFreq 1000
################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels $temperature
run 2500 ;# 5ps
.dat-file:
# xi A(xi) av_force n_samples
108.005 0.0000 0.0000 0
108.015 0.0000 0.0000 0
108.025 0.0000 0.0000 0
108.035 0.0000 0.0000 0
108.045 0.0000 0.0000 0
108.055 0.0000 0.0000 0
108.065 0.0000 0.0000 0
108.075 0.0000 0.0000 0
108.085 0.0000 0.0000 0
108.095 0.0000 0.0000 0
108.105 0.0000 0.0000 0
108.115 0.0000 0.0000 0
108.125 0.0000 0.0000 0
108.135 0.0000 0.0000 0
108.145 0.0000 0.0000 0
108.155 0.0000 0.0000 0
I really hope that anybody can help me!
greetings,
Christine
-- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:35 CST