about PMF and MCTI

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Fri May 11 2007 - 09:02:33 CDT

Hi all,
I read thread in the Mailing about free energy evaluation with PMF (Slow growth) and MCTI methods.
In NAMD user's guide ver 2.6 this one is not very well clarified argument.
Is there articles or tutorials or guides for these arguments?
How can read the output file ?
This is my input/output that work fine with some note:

# ...... Standard NPT molecular dynamics
# # Scripting

#freeEnergy on
#freeEnergyConfig {
#urestraint { ! Force Restrain in dihedral angle
#dihe pmf (O1,300,C62) (O1,300,C61) (O1,300,C6) (O1,300,C7) #barr=100.0low=52.0hi=140.0
# }
# mcti {
# task = stepup
# equiltime = 2000 fs ! T1
# accumtime = 8000 fs ! T2
# numsteps = 34 ! Number of Step for cycle: NC
# print= 2 ps
# }
#}
# numsteps 340150 ! Number of step of dynamic greater or equal to (T1+T2)xNC

OUTPUT:
nstep time(ps) task lambdaKf lambdaRef delta-G #steps n*{value target }
 --------------------- -------- --------- -------- ------ ----------------
  2000 2.000 StepUp 1.00000 0.02941 57.198 54.588 ! EquilTime
  4000 4.000 StepUp 1.00000 0.02941 8.94e-01 2000 53.376 54.588 ! AccumTime
  6000 6.000 StepUp 1.00000 0.02941 2.23e-01 4000 59.932 54.588 "
  8000 8.000 StepUp 1.00000 0.02941 -1.96e-01 6000 51.664 54.588 "
 10000 10.000 StepUp 1.00000 0.02941 -5.68e-01 8000 51.111 54.588 ! END Accumulation Time
 12000 12.000 StepUp 1.00000 0.05882 59.054 57.176 ! EquilTime
 14000 14.000 StepUp 1.00000 0.05882 4.63e-01 2000 52.546 57.176 ! AccumTime
 16000 16.000 StepUp 1.00000 0.05882 -2.11e+00 4000 65.906 57.176 ! "
 18000 18.000 StepUp 1.00000 0.05882 -4.00e+00 6000 75.797 57.176 ! "
 20000 20.000 StepUp 1.00000 0.05882 -4.21e+00 8000 60.124 57.176 ! END Accumulation Time

What is Delta-G?
Is Delta-G, at the END of accumulation time, free energy for target dihedral value?
Is free energy in kCal/mol ?

Best Regards
Luca

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:17 CST