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
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Received on Thu Nov 13 2003 - 12:53:01 PST
