Hello Hai,
Thanks for your tips. Actually, I am following the same protocol for a
similar system from a paper.
They also used a distance of 1.6 for the starting window. :-
All the best,
Qinghua
On 01/25/2017 04:52 PM, Nhai wrote:
> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Wed Jan 25 2017 - 08:30:03 PST
