Re: [AMBER] Is this output OK from the hybrid remd?

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 20 Dec 2010 11:53:51 -0500

If you just switched reference coordinates without re-running the
equilibration and such subject to the new reference coordinates, then the
errors that you were seeing in the exchange attempts you will start seeing
in the normal MD steps (and that's what you're seeing below). You actually
need to re-equilibrate in order to use the same reference structure.

Good luck,
Jason

On Sun, Dec 19, 2010 at 2:02 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:

> Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
>
> > this was asked before- you aren't using the same refc for all replicas.
> this
> > will not work unless you implement a Hamiltonian exchange method. it may
> not
> > be the only problem, but it certainly isn't going to be correct.
> > also a force constant of 5.0 is not a weak restraint like your label
> says,
> > it's a very strong one.
> > why do you have &ewald flags in the remd stage and not during
> equilibration?
> > On Sat, Dec 18, 2010 at 2:23 PM, Bongkeun Kim <bkim.chem.ucsb.edu>
> wrote:
> >
> I used the same refc, gr3252_min2.rst for remd and reduce the
> restraint from 5 to 1 and I got followings.
> .@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> =================HYBRID REMD: energy calc for exch
> 1=================
> HYBRID REMD: Stripping waters
> wrapping first mol.: 83.13530 81.46523 41.15202
> HYBRID REMD: New natom= 4820
> HYBRID REMD: Calling force.
>
> NSTEP = 0 TIME(PS) = 125.800 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot =
> 41639255.9775
> BOND = 21696.1073 ANGLE = 545430.9243 DIHED =
> 332.9894
> 1-4 NB = 52805.3954 1-4 EEL = 1810.6154 VDWAALS =
> -5399.3245
> EELEC = -6904.4819 EGB = -2947.5234 RESTRAINT =
> 41032431.2754
> EAMBER (non-restraint) = 606824.7021
> TEMP0 = 329.8000 REPNUM = 9 EXCHANGE# =
> 0
>
>
> ------------------------------------------------------------------------------
>
> HYBRID REMD: myEptot= ************ myTargetTemp= 329.80
> HYBRID REMD: Restoring...
> =========================END HYBRID REMD energy
> calc.=========================
> REMD: myEptot= 41639255.9775 myTargetTemp= 329.80 mytemp= 0.00
> ==========================REMD EXCHANGE
> CALCULATION==========================
> Exch= 1 RREMD= 0
> Replica Temp= 329.80 Indx= 9 Rep#= 9 EPot= **********
> Partner Temp= 323.80 Indx= 8 Rep#= 8 EPot= **********
> Not controlling exchange.
> Rand= 0.256064E+00 MyScaling= -1.00 Success= F
> ========================END REMD EXCHANGE
> CALCULATION========================
> REMD: checking to see if bath T has changed: 329.80->329.80
> | # 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 restraint energy decreased about order of 10 but still showed
> ************ on EPot. If I did anything wrong again, please let me know.
> Thank you.
> Bongkeun Kim
>
> >> Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> >>
> >> > we're still not sure what you restrained. did you use the same refc
> for
> >> all
> >> > of the remd runs? it isn't clear since you said below it was from the
> NPT
> >> > run- was that the equilibration right before remd, or something else?
> >> > why would you get a vacuum bubble? these are all NVT right?
> >> > On Sat, Dec 18, 2010 at 11:52 AM, Bongkeun Kim <bkim.chem.ucsb.edu>
> >> wrote:
> >> >
> >> I used one pdb file from the 100ns npt run and ran 200ps equilibrium
> >> md with the following input file.
> >> ++++++++++++++++++++++++++++++++++++++++++++=
> >> Equilibration
> >> &cntrl
> >> irest=0, ntx=1,
> >> nstlim=1000000, dt=0.0002,
> >> ntt=3, gamma_ln=1.0,
> >> temp0=XXXXX, ig=RANDOM_NUMBER,
> >> ntc=2, ntf=2, nscm=1000,
> >> ntb=1, ntr=1,
> >> cut=12.0,
> >> ntpr=500, ntwx=500, ntwr=1000,
> >> /
> >> Hold the GRA fixed
> >> 5.0
> >> RES 1 1346
> >> END
> >> END
> >> +++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> A part of group file looks like this.
> >> +++++++++++++++++++++++++++++++++++++++==
> >> -O -rem 0 -i equilibrate.mdin.001 -o equilibrate.mdout.001 -c
> >> gr3252_min2.rst -r equilibrate.rst.001 -x equilibrate.mdcrd.001 -inf
> >> equilibrate.mdinfo.001 -p gr3252.prmtop -ref gr3252_min2.rst
> >> -O -rem 0 -i equilibrate.mdin.002 -o equilibrate.mdout.002 -c
> >> gr3252_min2.rst -r equilibrate.rst.002 -x equilibrate.mdcrd.002 -inf
> >> equilibrate.mdinfo.002 -p gr3252.prmtop -ref gr3252_min2.rst
> >> -O -rem 0 -i equilibrate.mdin.003 -o equilibrate.mdout.003 -c
> >> gr3252_min2.rst -r equilibrate.rst.003 -x equilibrate.mdcrd.003 -inf
> >> equilibrate.mdinfo.003 -p gr3252.prmtop -ref gr3252_min2.rst
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> The input and groupfile of REMD is following:
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> Equilibration
> >> &cntrl
> >> irest=1, ntx=5,
> >> nstlim=500, dt=0.002,
> >> ntt=3, gamma_ln=1.0,
> >> temp0=XXXXX, ig=RANDOM_NUMBER,
> >> 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
> >>
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++==
> >> -O -rem 1 -remlog rem.log -i remd.mdin.001 -o remd.mdout.001 -c
> >> equilibrate.rst.001 -r remd.rst.001 -x remd.mdcrd.001 -inf
> >> remd.mdinfo.001 -p gr3252.prmtop -ref equilibrate.rst.001
> >> -O -rem 1 -remlog rem.log -i remd.mdin.002 -o remd.mdout.002 -c
> >> equilibrate.rst.002 -r remd.rst.002 -x remd.mdcrd.002 -inf
> >> remd.mdinfo.002 -p gr3252.prmtop -ref equilibrate.rst.002
> >> -O -rem 1 -remlog rem.log -i remd.mdin.003 -o remd.mdout.003 -c
> >> equilibrate.rst.003 -r remd.rst.003 -x remd.mdcrd.003 -inf
> >> remd.mdinfo.003 -p gr3252.prmtop -ref equilibrate.rst.003
> >>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> Please let me know what I can do to solve this problem.
> >> Thank you.
> >> Bongkeun Kim
> >>
> >> >>
> >> >> Quoting Jason Swails <jason.swails.gmail.com>:
> >> >>
> >> >> > The restraint energy is still outrageous, but I'm not quite sure
> what
> >> was
> >> >> > happening with your previous simulation without restraints. Since
> I
> >> >> didn't
> >> >> > write the hybrid remd code and I've never used it, I don't know how
> >> much
> >> >> > help I can be of here.
> >> >> >
> >> >> > However, Dave Case's point was a good one, and you never really
> >> answered
> >> >> > it. Did you use the same reference structure for each replica? If
> >> you
> >> >> > didn't, then this will cause your restraint energies to be very
> high
> >> as
> >> >> > well.
> >> >> I used the same structure from the single npt simulation about 100ns
> >> run.
> >> >> And I ran a group equilibrium md for all replicas in order to
> >> >> equilibrate each replica in each target temperature to avoid a vacuum
> >> >> bubble. the final rst files from this step were used to run remd. So
> >> >> do you think I have to run a hybrid REMD without running equil MD to
> >> >> use the same reference structure? If so, how do I avoid bubble in the
> >> >> space?
> >> >> Thank you.
> >> >> Bongkeun Kim
> >> >> >
> >> >> > Good luck!
> >> >> > Jason
> >> >> >
> >> >> > On Sat, Dec 18, 2010 at 12:00 AM, Bongkeun Kim <bkim.chem.ucsb.edu
> >
> >> >> wrote:
> >> >> >
> >> >> >> Hello,
> >> >> >>
> >> >> >> I applied this patch and used ntr=1 again.
> >> >> >> .@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> >> >> >> =================HYBRID REMD: energy calc for exch
> >> >> >> 1=================
> >> >> >> HYBRID REMD: Stripping waters
> >> >> >> wrapping first mol.: 83.13530 0.00000 41.15202
> >> >> >> HYBRID REMD: New natom= 4820
> >> >> >> HYBRID REMD: Calling force.
> >> >> >>
> >> >> >> NSTEP = 0 TIME(PS) = 127.600 TEMP(K) = 0.00
> PRESS
> >> >> >> = 0.0
> >> >> >> Etot = 0.0000 EKtot = 0.0000 EPtot =
> >> >> >> 116431771.4632
> >> >> >> BOND = 22423.0668 ANGLE = 546043.1091 DIHED =
> >> >> >> 388.7305
> >> >> >> 1-4 NB = 52961.7061 1-4 EEL = 1814.5928 VDWAALS =
> >> >> >> -5494.9108
> >> >> >> EELEC = -6066.5669 EGB = -3141.0101 RESTRAINT =
> >> >> >> 115822842.7455
> >> >> >> EAMBER (non-restraint) = 608928.7177
> >> >> >> TEMP0 = 501.0000 REPNUM = 32 EXCHANGE# =
> >> >> >> 0
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------
> >> >> >>
> >> >> >> HYBRID REMD: myEptot= ************ myTargetTemp= 501.00
> >> >> >> HYBRID REMD: Restoring...
> >> >> >> =========================END HYBRID REMD energy
> >> >> >> calc.=========================
> >> >> >> REMD: myEptot= 116431771.4632 myTargetTemp= 501.00 mytemp= 0.00
> >> >> >> ==========================REMD EXCHANGE
> >> >> >> CALCULATION==========================
> >> >> >> Exch= 1 RREMD= 0
> >> >> >> Replica Temp= 501.00 Indx= 32 Rep#= 32 EPot= **********
> >> >> >> Partner Temp= 285.10 Indx= 1 Rep#= 1 EPot= **********
> >> >> >> Metrop= 0.000000E+00 delta= 0.181951E+04 o_scaling=
> >> -1.00
> >> >> >> Rand= 0.821770E+00 MyScaling= -1.00 Success= F
> >> >> >> ========================END REMD EXCHANGE
> >> >> >> CALCULATION========================
> >> >> >> REMD: checking to see if bath T has changed: 501.00->501.00
> >> >> >> | # 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.
> >> >> >> vlimit exceeded for step 8; vmax = 135.1554
> >> >> >> vlimit exceeded for step 10; vmax = 98.9017
> >> >> >> .@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> >> >> >>
> >> >> >> So, there is only one ****** on HYBRID REMD: myEptot= ************
> >> >> >> and EPtot is still large but is not ****. Because EPtot is too
> large,
> >> >> >> I'm afraid that exchanges occur or not.
> >> >> >> How do you think this output.
> >> >> >> Thank you.
> >> >> >> Bongkeun Kim
> >> >> >>
> >> >> >> Quoting Jason Swails <jason.swails.gmail.com>:
> >> >> >>
> >> >> >> > Hello,
> >> >> >> >
> >> >> >> > I think your problem lies in the use of coordinate restraints
> with
> >> >> hybrid
> >> >> >> > REMD. One of the steps that hybrid REMD has to do is reimage
> all
> >> of
> >> >> the
> >> >> >> > water molecules and place it at the location of its closest
> >> periodic
> >> >> >> image
> >> >> >> > since GB methods are inherently non-periodic and know nothing
> about
> >> >> >> > alternate images.
> >> >> >> >
> >> >> >> > One of the things done in "subroutine stripwat" in remd.f is the
> >> >> >> centering
> >> >> >> > of the entire system with respect to its center of mass. The
> >> reason I
> >> >> >> think
> >> >> >> > you are having issues is that the coordinates are adjusted by
> the
> >> >> center
> >> >> >> of
> >> >> >> > mass position, but the reference coordinates are never adjusted.
> >> >> >> >
> >> >> >> > I'm not positive this will work, but I included a patch which
> will
> >> >> adjust
> >> >> >> > the reference coordinates in exactly the same way as the normal
> >> >> >> > coordinates. Apply it to the latest, fully patched amber11 from
> >> >> >> AMBERHOME.
> >> >> >> >
> >> >> >> > cd $AMBERHOME
> >> >> >> > patch -p0 -N < hybrid_remd.patch
> >> >> >> >
> >> >> >> > Then recompile. Also please report back whether it worked or
> not.
> >> >> One
> >> >> >> > other thing to try that probably should've been mentioned before
> is
> >> >> >> testing
> >> >> >> > to see that it worked if you don't include restraints, just to
> make
> >> >> sure
> >> >> >> > that it is in fact the restraints that are causing the issue.
> >> >> >> >
> >> >> >> > Hope this helps,
> >> >> >> > Jason
> >> >> >> >
> >> >> >> > On Fri, Dec 17, 2010 at 11:43 AM, Bongkeun Kim <
> bkim.chem.ucsb.edu
> >> >
> >> >> >> wrote:
> >> >> >> >
> >> >> >> >> Quoting case <case.biomaps.rutgers.edu>:
> >> >> >> >>
> >> >> >> >> > On Fri, Dec 17, 2010, Bongkeun Kim wrote:
> >> >> >> >> >>
> >> >> >> >> >> 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?
> >> >> >> >> >
> >> >> >> >> > There seems to be a problem with the restraint energy:
> >> >> >> >> >
> >> >> >> >> >> EELEC = -6589.2279 EGB = -3004.6220
> RESTRAINT
> >> >> >> >> >> =57092146.9150
> >> >> >> >> >
> >> >> >> >> > You can't run replica exchange simulations with ntr>0
> (unless, I
> >> >> >> guess,
> >> >> >> >> that
> >> >> >> >> > all replicas have the same reference structure. Also, be
> sure
> >> that
> >> >> >> you
> >> >> >> >> can
> >> >> >> >> > sucessfully run non-exchange simulations at each temperature
> of
> >> >> >> interest.
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >> I already tried to run it with full explicit water and it gave
> me
> >> no
> >> >> >> >> problem. But this run demands too many resources.
> >> >> >> >>
> >> >> >> >> With hybridgb, EPtot = 58053860.3203 and
> >> >> >> >> Without hybbridgb, EPtot = 546283.2545.
> >> >> >> >>
> >> >> >> >> Also, RESTRAINT = 57444151.6840 with hybridgb and
> >> >> >> >> RESTRAINT = 177.4334 without hybridgb.
> >> >> >> >> It seems like the hybridgb method overestimates restraint
> energy
> >> of
> >> >> my
> >> >> >> >> graphite surface too much. I checked the structure of whole
> >> system.
> >> >> >> >> The peptide lies on the graphite surface now. I think
> explicitly
> >> >> >> >> considered water molecules by numwatkeep=500 are on the other
> side
> >> of
> >> >> >> >> graphite surface, that is across the surface. Do you think this
> >> makes
> >> >> >> >> problems?
> >> >> >> >> Thank you.
> >> >> >> >> Bongkeun Kim
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> _______________________________________________
> >> >> >> >> AMBER mailing list
> >> >> >> >> AMBER.ambermd.org
> >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >>
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > Jason M. Swails
> >> >> >> > Quantum Theory Project,
> >> >> >> > University of Florida
> >> >> >> > Ph.D. Graduate Student
> >> >> >> > 352-392-4032
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Jason M. Swails
> >> >> > Quantum Theory Project,
> >> >> > University of Florida
> >> >> > Ph.D. Graduate Student
> >> >> > 352-392-4032
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> _______________________________________________
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> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >>
> >>
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> >>
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> >
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>
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-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Dec 20 2010 - 09:00:03 PST
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