Hi Vinicius
Thank you for your suggestion. 40 ns would be long time for serial mode.
My system is of just 120 atoms, I am not sure parallel run would be more
effective in terms of speed.
Santo
On Wed, 22 Jan 2020 at 02:44, Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
wrote:
> Hello Santo,
>
> I suspect your issue is in the fact that you are running the production
> phase with only 4 ns. I suggest you to run a 4 ns simulation
> (outside finddgref.py) with one of the DELTAGREF values in the log file you
> sent and then use the --cumulative option in cphstats to check the
> convergence of your fraction of protonated species. I strongly suspect that
> this analysis will show that 4 ns is not enough to converge.
>
> If that is indeed the case, you will need to increase the total number of
> steps in your mdin file (I would try 40 ns, as a first trial). If you have
> access to more CPUs, you would gain significantly in sampling and in
> accuracy by running finddgref.py in parallel mode, which makes use of
> pH-REMD.
>
> I hope this helps,
> Best,
>
> *VinÃcius Wilian D. Cruzeiro*
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
> ------------------------------
> *From:* Kolattukudy P. Santo <santotheophys.gmail.com>
> *Sent:* Tuesday, January 21, 2020 9:13 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] convergence of Ref energies in cpHMD
>
> [External Email]
>
> 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
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=cXy6VPDsXJaEMYpImZJu4R0K7Ri2m1idUh27vINEsVs&s=athAkYfSK3HAZiHL5IbmbwIO8OMH4u1ukbIHGrjkn2U&e=
> >
>
>
> --
> *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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>
--
*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 Wed Jan 22 2020 - 07:00:03 PST
