On Wed, Jan 25, 2017, Qinghua Liao wrote:
>
> 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
>
Use LISTIN=POUT (say, right before the "DISANG=" line): this will print out
details of the all of the restraints after they are read in, so you can check
the input.
Beyond that: do you have a bond between atom 345 and atom 425? If not, you
are fighting the non-bonded repulsion between these two atoms, and no
(reasonable) harmonic restraint will force you to a 1.6 Ang. distance.
In fact, would probably get what you describe: distances that are around
1.9 or 2.0 Angstroms.
So: if you manually create a structure with a 1.6 Ang. distance, what force
field energy do you get?
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 25 2017 - 11:30:02 PST
