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
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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>>>>>
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Received on Wed Jan 25 2017 - 11:00:02 PST
