AMBER Archive (2003)

Subject: AMBER: GIBBS - PMF problem: Lambda has not changed

From: Jiri Matousek (matousek_at_chemi.muni.cz)
Date: Thu Nov 13 2003 - 06:32:01 CST

Hi Amber users,
I am trying to do free energy calculation using PMF. The change in
conformation depends on one distance, so I have one constraint. Problem
is that lambda ( ... distance) is all the time at the starting value.
  I mostly used TI, but I tryied nearly all methods (by chaging isldyn)
with the same results. No error message appered during my calculation,
so I really have no suggestion what is wrong in my input file.
Any answer will be very helpfull.
Thank you in advance.

Jiri Matousek

Here is my input file and MICSTAT:

input:
#pokus
  &cntrl
  ntx=7,
  ntb=2,
  ntp=1,
  ntwx=250,
  ntwe=250,
  isande=1,
  ntpr=250,
  scee=1.2,
  cut=15.0,
  temp0=300,
  taup=1.0,

  dt=0.002,

  ntc=2,
  ntf=2,

  ntt=1,
  tautp=0.2,
  nscm=-1,

  nrun=11,
  nstlim=100,

  isldyn=3,
  idifrg=1,
  almda=0.0,
  almdel=0.1,
  nstmeq=30,
  nstmul=70,

  ncorc=1,
  intr=1,
  itimth=1,
  &end
    14 41 0 0 0 0 2 0.00000 1.00000
  100.00000 5.40000 100.00000 10.40000 0 0

MICSTAT:
  #pokus
                                                   /FREE ENERGIES/
                 FORWARD # STEPS EQUILIBRATION DATA
COLLECTION
  WIND LAMBDA dLAMBDA NR EQ COLL FORWARD REVERSE FORWARD
REVERSE
     1 0.000000 0.000000 0 30 70
     2 0.000000 0.000000 0 30 70
     3 0.000000 0.000000 0 30 70
     4 0.000000 0.000000 0 30 70
     5 0.000000 0.000000 0 30 70
     6 0.000000 0.000000 0 30 70
     7 0.000000 0.000000 0 30 70
     8 0.000000 0.000000 0 30 70
     9 0.000000 0.000000 0 30 70
    10 0.000000 0.000000 0 30 70
    11 0.000000 0.000000 0 30 70

                                   *SUMMARY*
                                                    FREE ENERGIES
                                     # STEPS DATA COLLECTION
                          AVE TOT AVE AVE TOTAL
  WIND STEPS LAMBDA dLAMBDA NR EQ COLL FORWARD
    11 1100 0.00-0.00 0.000000 0 30 70 0.0000

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu