1.6 A is very close to bond length.
Hai
Hai Nguyen
> On Jan 25, 2017, at 10:49 AM, Carlos Simmerling <carlos.simmerling.gmail.com> 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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Received on Wed Jan 25 2017 - 08:00:03 PST
