TMD simulations

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Fri Apr 30 2010 - 02:52:52 CDT

Dear NAMD users
 
 

I carried out TMD simulations of a polypeptide of hemaglutinin. I was analysing log file but I do not know what the third and fourth columns means. I think the last one has information about rmsd respect target structure, but i am not sure. I wait somebody can help me with it. Thanks
Andres
 
ENERGY: 0 123.9492 325.1711 158.8218 15.9574 -87899.1085 8291.3290 0.0000 0.0000 13820.6814 -65163.1986 298.3264 -65155.0510 -65155.0510 298.3264
TMD 1 14.773 14.7732
TMD 2 14.7728 14.7732
TMD 3 14.7727 14.7733
TMD 4 14.7725 14.7733
TMD 5 14.7724 14.7733
TMD 6 14.7722 14.7732
TMD 7 14.7721 14.773
TMD 8 14.7719 14.7727
TMD 9 14.7718 14.7724
TMD 10 14.7716 14.7719
 
 
I used the following script to run the simulation:
 
#############################################################
## JOB DESCRIPTION ##
#############################################################
 
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure 1hgf.psf
coordinates 1hgf.pdb
bincoordinates 1hgf_equil.coor
binvelocities 1hgf_equil.vel
 
set outputname TMD_nomin
firsttimestep 0
numsteps 100000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all22_prot.inp
 
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
margin 0
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# Output
outputName $outputname
dcdfreq 1000
outputEnergies 10
 
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Boundary conditions
#wrapWater on
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
 
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Targeted
TMD on
TMDk 200
TMDFirstStep 0
TMDLastStep 100000
TMDfile 1htm_equil.pdb
TMDFinalRMSD 0

                                               
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