I applied all the bug fix already.
Thanks.
Quoting Jason Swails <jason.swails.gmail.com>:
> Make sure all bug fixes are applied. One was just issued for hybrid REMD.
> http://ambermd.org/bugfixes11.html See bugfix.10.
>
> Good luck!
> Jason
>
> On Fri, Dec 17, 2010 at 3:13 AM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>
>> Hello,
>>
>> I just run the hybrid remd and checked the output file.
>> It said ********** on EPot. Does it mean only the number is too big to
>> print or is there any problem on this run?
>> -------------------------------------------------
>> REMD: checking to see if bath T has changed: 290.40->295.70
>> REMD: scaling velocities by 1.009 to match new bath T 295.700
>> | # of SOLUTE degrees of freedom (RNDFP): 59256.
>> | # of SOLVENT degrees of freedom (RNDFS): 0.
>> | NDFMIN = 59256. NUM_NOSHAKE = 0 CORRECTED RNDFP =
>> 59256.
>> | TOTAL # of degrees of freedom (RNDF) = 59256.
>>
>> NSTEP = 500 TIME(PS) = 127.600 TEMP(K) = 292.12 PRESS
>> = 0.0
>> Etot = 546279.5847 EKtot = 17198.9654 EPtot =
>> 529080.6192
>> BOND = 21696.8949 ANGLE = 545342.5334 DIHED =
>> 344.3322
>> 1-4 NB = 52807.9864 1-4 EEL = 1814.0585 VDWAALS =
>> 1821.9233
>> EELEC = -94866.3887 EHBOND = 0.0000 RESTRAINT =
>> 119.2792
>> EAMBER (non-restraint) = 528961.3400
>> Ewald error estimate: 0.9463E-04
>> TEMP0 = 295.7000 REPNUM = 1 EXCHANGE# =
>> 3
>>
>>
>> ------------------------------------------------------------------------------
>>
>> =================HYBRID REMD: energy calc for exch
>> 4=================
>> HYBRID REMD: Stripping waters
>> wrapping first mol.: 83.13530 0.00000 41.15202
>> HYBRID REMD: New natom= 4820
>> HYBRID REMD: Calling force.
>>
>> NSTEP = 500 TIME(PS) = 127.600 TEMP(K) = 292.12 PRESS
>> = 0.0
>> Etot = 546279.5847 EKtot = 17198.9654 EPtot =
>> 57699058.5630
>> BOND = 21725.4188 ANGLE = 545334.2328 DIHED =
>> 343.4305
>> 1-4 NB = 52805.6877 1-4 EEL = 1812.3603 VDWAALS =
>> -5515.6322
>> EELEC = -6589.2279 EGB = -3004.6220 RESTRAINT =
>> 57092146.9150
>> EAMBER (non-restraint) = 606911.6480
>> TEMP0 = 295.7000 REPNUM = 1 EXCHANGE# =
>> 3
>>
>>
>> ------------------------------------------------------------------------------
>>
>> HYBRID REMD: myEptot= ************ myTargetTemp= 295.70
>> HYBRID REMD: Restoring...
>> =========================END HYBRID REMD energy
>> calc.=========================
>> REMD: myEptot= 57699058.5630 myTargetTemp= 295.70 mytemp= 292.12
>> ==========================REMD EXCHANGE
>> CALCULATION==========================
>> Exch= 4 RREMD= 0
>> Replica Temp= 295.70 Indx= 3 Rep#= 1 EPot= **********
>> Partner Temp= 301.10 Indx= 4 Rep#= 7 EPot= **********
>> Not controlling exchange.
>> Rand= 0.376598E+00 MyScaling= 1.01 Success= T
>> ========================END REMD EXCHANGE
>> CALCULATION========================
>> REMD: checking to see if bath T has changed: 295.70->301.10
>> REMD: scaling velocities by 1.009 to match new bath T 301.100
>> | # of SOLUTE degrees of freedom (RNDFP): 59256.
>> | # of SOLVENT degrees of freedom (RNDFS): 0.
>> | NDFMIN = 59256. NUM_NOSHAKE = 0 CORRECTED RNDFP =
>> 59256.
>> | TOTAL # of degrees of freedom (RNDF) = 59256.
>> -------------------------------------------------------------------
>>
>> The input file looks like this:
>> Equilibration
>> &cntrl
>> irest=1, ntx=5,
>> nstlim=500, dt=0.002,
>> ntt=3, gamma_ln=1.0,
>> temp0=285.1, ig=11052,
>> ntp=0, pres0= 1.0, taup=2.0,
>> ntc=2, ntf=2, nscm=1000,
>> ntb=1, igb=0,
>> hybridgb=5, numwatkeep= 500,
>> ntr=1,
>> cut=12.0,
>> ntpr=500, ntwx=1000, ntwr=1000,
>> nmropt=0,
>> numexchg=4000,
>> /
>> &ewald
>> nfft1 = 96,
>> nfft2 = 96,
>> nfft3 = 96,
>> order = 4,
>> verbose = 0,
>> ew_type = 0,
>> nbflag = 1,
>> skinnb = 2.0,
>> netfrc = 1,
>> vdwmeth = 1,
>> column_fft = 1,
>> /
>> Keep GRA fixed with weak restraints
>> 5.0
>> FIND
>> * * * GRA
>> SEARCH
>> RES 1 1346
>> END
>> END
>> +++++++++++++++++++++++++++++++++++++++++++++++
>>
>> Epot has a value around 545271.22 without using this hybrid gb method.
>> And introducing hybridgb makes this large number problem.
>> If you have any description about it, please let me know.
>> Thank you.
>> Bongkeun Kim
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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>
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Received on Fri Dec 17 2010 - 08:30:07 PST
