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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Received on Fri Dec 17 2010 - 05:00:06 PST
