Dear Prof. Roitberg,
I am sorry for the confusion resulted from my typo. And also thanks very
much
for your explanation on the source of the difference of restraints. Then
it makes
sense to me! Thanks a lot!
All the best,
Qinghua
On 01/25/2017 07:45 PM, Adrian Roitberg wrote:
>
> On 1/25/17 1:40 PM, Qinghua Liao wrote:
>> Dear Prof. Roitberg,
>>
>> Thanks very much for your reply!
>>
>> The distance of 2.091 angstrom was reported by pemed,
>> which was included in a separate file, distance.dat.
>>
>> The restraint file was included in a previous e-mail, as follows:
>>
>> 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
>>
>>
>> I followed the tutorial, and also checked the manual. I hope that
>> my settings are correct. Thanks!
>>
>>
>> All the best,
>> Qinghua
> ok, you had written bellow a distance of 2.91 and that was puzzling
> 2.091 is much closer to what is supposed to be.
>
> Anyways, if you ask WHAT should the distance be to get a restraint
> energy of 100 kcal/mol, the answer is 2.047 A, which is very close to
> your 2.091
> I am pretty sure the difference comes from which steps is reported in
> the distance file vs the mdout file. They are probably shifted by one step.
> adrian
>
>
>>
>> On 01/25/2017 06:52 PM, Adrian Roitberg wrote:
>>> How do you know that the distance is 2.91 ?
>>>
>>> The trajectory file and the mdout are displaced by one step.
>>>
>>> In any case, what was your restraint file? What the values of r1,r2,r3
>>> and r4 and the respective rk?
>>>
>>> adrian
>>>
>>>
>>>
>>> On 1/25/17 12:46 PM, Carlos Simmerling wrote:
>>>> 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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Received on Wed Jan 25 2017 - 11:00:04 PST
