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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Wed Jan 25 2017 - 11:00:03 PST
