if the energy for that distance is 100 kcal, it is very strained. be aware
that increasing your force constant might lead to system instability unless
you reduce your time step. I would wonder if it is needed to sample a
distance that close when the energy is so high.
On Wed, Jan 25, 2017 at 11:10 AM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:
> Dear Carlos,
>
> Thanks very much for your reply. I have checked the output file, and it
> told me
> that pmemd read the restraints successfully:
>
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> DUMPFREQ 50 0 0.000000 0.000000 0 0
> ** No weight changes given **
>
> RESTRAINTS:
> Requested file redirections:
> DISANG = restraints.dat
> DUMPAVE = distance.dat
> Restraints will be read from file: restraints.dat
> Here are comments from the DISANG input file:
>
> Number of restraints read = 1
>
> Done reading weight changes/NMR restraints
>
> But I did not see the atom numbers, on which the restraints should be
> applied.
> One of my coworkers tell me that amber would report it for the older
> versions.
>
>
> At step 5000, the distance of two oxygen atoms from two water molecules
> is 2.091 angstrom.
> and the output is:
>
> NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 298.09 PRESS =
> -440.1
> Etot = -8258.9809 EKtot = 1691.8138 EPtot = -9950.7947
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> 1902.7228
> EELEC = -11962.9568 EHBOND = 0.0000 RESTRAINT =
> 109.4393
> EAMBER (non-restraint) = -10060.2340
> EKCMT = 881.2864 VIRIAL = 1248.8945 VOLUME =
> 38686.1037
> Density =
> 0.7362
> Ewald error estimate: 0.5317E-04
> ------------------------------------------------------------
> ------------------
>
> NMR restraints: Bond = 109.439 Angle = 0.000 Torsion = 0.000
> ============================================================
> ===================
>
>
>
> As the force constant is 500 kcal/mol, the restraints energy should be
> 500*(2.91-1.60)**2 kcal/mol = 120.5 kcal/mol.
> It is close to the one in the output, though I don't know where does the
> difference come from.
>
>
>
> All the best,
> Qinghua
>
>
> On 01/25/2017 04:49 PM, Carlos Simmerling wrote:
> > 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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> >>
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>
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Received on Wed Jan 25 2017 - 10:00:02 PST
