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

From: Bongkeun Kim <bkim.chem.ucsb.edu>
Date: Mon, 20 Dec 2010 09:30:43 -0800

Quoting Jason Swails <jason.swails.gmail.com>:

> 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.
>
I used a single reference structure during the equilibration md which
is gr3252_min2.rst. Only thing I did is I changed the reference
structure from each final output of eq md for each replica to this
gr3252_min2.rst.
Thank you.
Bongkeun Kim

> 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
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> _______________________________________________
>> >> >> AMBER mailing list
>> >> >> AMBER.ambermd.org
>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >> >>
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>>
>>
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>





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