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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Received on Fri Dec 17 2010 - 00:30:02 PST
