Hi Vinicius
The mdin file is:
-------------------
Implicit solvent constant pH molecular dynamics
&cntrl
imin=0, irest=1, ntx=5,
ntpr=1000, ntwx=1000, nstlim=2000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, tautp=2.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=30,
ntb=0, igb=2, saltcon=0.1,
nrespa=1, tol=0.000001, icnstph=1,
solvph=4.5, ntcnstph=5,
gamma_ln=5.0, ntwr=10000, ioutfm=1,
/
----------------------------
The initial log file was deleted. The currently running log file ( still
running ) is below. This has been running for about 15 hours.
-----------------
Checking cpin file and/or cein file.
We are going to find DELTAGREF for a pH titratable residue without using
Replica Exchange.
The solvent pH value is 4.500 and was loaded from the mdin file (
finddg.in).
The temperature is 300.00 K and was loaded from the mdin file (finddg.in
).
According to the mdin file (finddg.in), the value of ntcnstph is 5.
According to the mdin file (finddg.in), the value of nstlim is 2000000.
The program will try to find a range of values for DELTAGREF
automatically, as the argument -dgrefrange was not given
AMBER execution #1: running 50 MD steps for DELTAGREF = 0.000000 kcal/mol
The fraction of protonated species is 0.00% for the Residue 'UAP 2'
AMBER execution #2: running 50 MD steps for DELTAGREF = -100.000000
kcal/mol
The fraction of protonated species is 0.00% for the Residue 'UAP 2'
AMBER execution #3: running 50 MD steps for DELTAGREF = 100.000000 kcal/mol
The fraction of protonated species is 100.00% for the Residue 'UAP 2'
The value of DELTAGREF in which 20% > fraction of protonated species > 80%
for solvent pH = 4.5 is between 0.000000 and 100.000000 kcal/mol.
AMBER execution #4: running 200 MD steps for DELTAGREF = 50.000000 kcal/mol
The fraction of protonated species is 100.00% for the Residue 'UAP 2'
AMBER execution #5: running 200 MD steps for DELTAGREF = 25.000000 kcal/mol
The fraction of protonated species is 100.00% for the Residue 'UAP 2'
AMBER execution #6: running 200 MD steps for DELTAGREF = 12.500000 kcal/mol
The fraction of protonated species is 5.10% for the Residue 'UAP 2'
AMBER execution #7: running 200 MD steps for DELTAGREF = 18.750000 kcal/mol
The fraction of protonated species is 100.00% for the Residue 'UAP 2'
AMBER execution #8: running 200 MD steps for DELTAGREF = 15.625000 kcal/mol
The fraction of protonated species is 28.20% for the Residue 'UAP 2'
From this step on, we will make more accurate estimatives of DELTAGREF
values and we will keep increasing the number of steps.
The convergence criterium is: 48.50% >= fraction >= 51.50% for pH = 4.5.
AMBER execution #9: running 200000 MD steps of equilibration for
DELTAGREF = 16.182147 kcal/mol
AMBER execution #9: running 2000000 MD steps of production for
DELTAGREF = 16.182147 kcal/mol
The fraction of protonated species is 99.90% for the Residue 'UAP 2'
AMBER execution #10: running 200000 MD steps of equilibration for
DELTAGREF = 12.064631 kcal/mol
AMBER execution #10: running 2000000 MD steps of production for
DELTAGREF = 12.064631 kcal/mol
The fraction of protonated species is 7.00% for the Residue 'UAP 2'
AMBER execution #11: running 200000 MD steps of equilibration for
DELTAGREF = 13.606706 kcal/mol
AMBER execution #11: running 2000000 MD steps of production for
DELTAGREF = 13.606706 kcal/mol
The fraction of protonated species is 95.50% for the Residue 'UAP 2'
AMBER execution #12: running 200000 MD steps of equilibration for
DELTAGREF = 11.785415 kcal/mol
AMBER execution #12: running 2000000 MD steps of production for
DELTAGREF = 11.785415 kcal/mol
The fraction of protonated species is 3.80% for the Residue 'UAP 2'
AMBER execution #13: running 200000 MD steps of equilibration for
DELTAGREF = 13.711856 kcal/mol
AMBER execution #13: running 2000000 MD steps of production for
DELTAGREF = 13.711856 kcal/mol
The fraction of protonated species is 82.70% for the Residue 'UAP 2'
AMBER execution #14: running 200000 MD steps of equilibration for
DELTAGREF = 12.779159 kcal/mol
AMBER execution #14: running 2000000 MD steps of production for
DELTAGREF = 12.779159 kcal/mol
The fraction of protonated species is 35.50% for the Residue 'UAP 2'
AMBER execution #15: running 200000 MD steps of equilibration for
DELTAGREF = 13.135145 kcal/mol
AMBER execution #15: running 2000000 MD steps of production for
DELTAGREF = 13.135145 kcal/mol
The fraction of protonated species is 78.30% for the Residue 'UAP 2'
AMBER execution #16: running 200000 MD steps of equilibration for
DELTAGREF = 12.370134 kcal/mol
AMBER execution #16: running 2000000 MD steps of production for
DELTAGREF = 12.370134 kcal/mol
The fraction of protonated species is 12.90% for the Residue 'UAP 2'
AMBER execution #17: running 200000 MD steps of equilibration for
DELTAGREF = 13.508694 kcal/mol
AMBER execution #17: running 2000000 MD steps of production for
DELTAGREF = 13.508694 kcal/mol
The fraction of protonated species is 54.20% for the Residue 'UAP 2'
AMBER execution #18: running 200000 MD steps of equilibration for
DELTAGREF = 13.408303 kcal/mol
AMBER execution #18: running 2000000 MD steps of production for
DELTAGREF = 13.408303 kcal/mol
The fraction of protonated species is 51.70% for the Residue 'UAP 2'
AMBER execution #19: running 200000 MD steps of equilibration for
DELTAGREF = 13.367748 kcal/mol
AMBER execution #19: running 2000000 MD steps of production for
DELTAGREF = 13.367748 kcal/mol
The fraction of protonated species is 60.90% for the Residue 'UAP 2'
AMBER execution #20: running 200000 MD steps of equilibration for
DELTAGREF = 13.103584 kcal/mol
AMBER execution #20: running 2000000 MD steps of production for
DELTAGREF = 13.103584 kcal/mol
The fraction of protonated species is 35.60% for the Residue 'UAP 2'
AMBER execution #21: running 200000 MD steps of equilibration for
DELTAGREF = 13.456968 kcal/mol
AMBER execution #21: running 2000000 MD steps of production for
DELTAGREF = 13.456968 kcal/mol
The fraction of protonated species is 92.30% for the Residue 'UAP 2'
AMBER execution #22: running 200000 MD steps of equilibration for
DELTAGREF = 11.976217 kcal/mol
AMBER execution #22: running 2000000 MD steps of production for
DELTAGREF = 11.976217 kcal/mol
Thanks
Santo
On Mon, 20 Jan 2020 at 17:27, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> Hello Santo,
>
> May you send the mdin file you are using in the simulation and your
> current finddg.log file?
>
> Thanks,
>
>
> VinÃcius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633<tel:+1(352)846-1633>
>
> On Jan 20, 2020, at 12:42 PM, Kolattukudy P. Santo <
> santotheophys.gmail.com<mailto:santotheophys.gmail.com>> wrote:
>
> finddg.log
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Kolattukudy P. Santo*
*Post doctoral Associate *
*Department of Chemical and Biochemical Engineering*
*Rutgers, The State University of New Jersey*
*New Brunswick, New jersey*
*USA*
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Received on Tue Jan 21 2020 - 06:30:03 PST
