Hello,
I am doing umbrella sampling with amber16, the reaction coordinates are
the distances
between a metal ion and an oxygen of a water molecule. But I found that
the distance restraints
were failed for some windows. Here are my input files:
&cntrl
imin = 0, nstlim = 25000, irest = 0, ntx = 1, dt = 0.002 ,
ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
ntp = 1, pres0 = 1.0, taup = 2.0,
ntb = 2, cut = 12.0 ,
ntc = 2, ntf = 1,
iwrap = 1, nmropt = 1 ,
ntwe = 5000, ntwx = 5000, ntpr = 5000, ntwr = 5000,
/
&wt
type='DUMPFREQ', istep1=50, /
&wt
type='END',
&end
DISANG=restraints.dat
DUMPAVE=distance.dat
Harmonic restraints for distance of 1.6 angstrom
&rst
iat=345,425,
r1=0, r2= 1.6, r3= 1.6, r4=5.0,
rk2= 500.0 , rk3= 500.0 ,
&end
What I got for the distances from the simulation are around 2.0
angstrom, it never approaches 1.6 angstrom.
I even tried with a much higher force constant like 1000 kcal/mol A2,
then the distances go to around 1.9 angstrom,
but still not 1.6. However, the restraints are working for those windows
with restrained distances more than 2 angstrom.
Then I also try to restrain a distance between two water molecules at a
distance of 1.6, the restraints was also failed.
Similarly, it worked if I want to restrain the distance at 3.0 angstrom.
This is strange to me. Though we may think that the interaction between
a water molecule and the metal ion could be very
strong, a force constant of 500 or even 1000 kcal/mol A2 should make it
work. Could someone help me out of the problem?
Any response will be highly appreciated!
All the best,
Qinghua
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 25 2017 - 08:00:02 PST
