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:
>
So does it mean that I need to use only one reference structure such
as gr3252_min2.rst for all equil MD and REMD replicas?
I'm going to do equil md again and see any further problem happening or not.
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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>> >>
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>> >
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>>
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>>
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Received on Sun Dec 19 2010 - 11:00:05 PST
