what does your MD output say about the restraints? It should tell you if it
read them, and also the energies will tell you how much restraint strain
you have.
On Wed, Jan 25, 2017 at 10:44 AM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:
> 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
>
>
>
>
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Received on Wed Jan 25 2017 - 08:00:02 PST
