Dear Carlos,
Thanks very much for your reply! Yeah, I am also thinking of doing the
samplings
starting at a bigger distance. The simulation crashed when the force
constant increased.
Force constants of 500 or 1000 kcal/mol A2 are just for checking. 150
kcal/mol A2 was
used in the umbrella sampling, according to a previous paper.
All the best,
Qinghua
On 01/25/2017 06:46 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 - 11:00:02 PST
