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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 21 Dec 2010 17:33:21 -0500

Hi,

I think I've tracked this thing down - attached is a patch that should
fix the behavior of reference coordinates when hybridgb is in use. As
Jason had previously mentioned, the problem was with the treatment of
reference coordinates during the water stripping routine. However, his
patch resulted in the reference coordinates being modified without
restoring them after the GB calculation was complete. The attached
patch creates temporary storage for the reference coords, modifies the
reference coords using stripwat(), then restores them after the
force() call. I've done some testing here and things seem ok - let me
know if the patch doesn't work for you.

I also increased the width of the output energy in the "HYBRID REMD:
myEptot=" line, which should fix the ***** issue.

-Dan

On Mon, Dec 20, 2010 at 2:35 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> The previous data was from the last patch.
> I also tested this one without your patch again.
> The restraint energy is going up again.
> Thank you.
> Bongkeun Kim
> .@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> =================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) =     124.600  TEMP(K) =     0.00  PRESS
> =     0.0
>  Etot   =         0.0000  EKtot   =         0.0000  EPtot      =
> 12029643.8763
>  BOND   =     21452.3217  ANGLE   =    545232.3866  DIHED      =
>  337.2216
>  1-4 NB =     52797.7673  1-4 EEL =      1810.9335  VDWAALS    =
> -5472.0897
>  EELEC  =     -6564.7773  EGB     =     -3058.1446  RESTRAINT  =
> 11423108.2572
>  EAMBER (non-restraint)  =    606535.6191
>  TEMP0  =       285.1000  REPNUM  =              1  EXCHANGE#  =
>         0
>
> ------------------------------------------------------------------------------
>
> HYBRID REMD: myEptot= ************ myTargetTemp= 285.10
> HYBRID REMD: Restoring...
> =========================END HYBRID REMD energy calc.=========================
> REMD: myEptot=   12029643.8763 myTargetTemp= 285.10 mytemp=   0.00
> ==========================REMD EXCHANGE CALCULATION==========================
> Exch=          1 RREMD= 0
> Replica          Temp= 285.10 Indx=  1 Rep#=  1 EPot= **********
> Partner          Temp= 501.00 Indx= 32 Rep#= 32 EPot= **********
> Not controlling exchange.
> Rand=       0.798109E+00 MyScaling=      -1.00 Success= F
> ========================END REMD EXCHANGE CALCULATION========================
> .@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> Quoting Jason Swails <jason.swails.gmail.com>:
>
>> Is this with or without the patch that I sent earlier?  If it's without the
>> patch applied and compiled then try applying the patch and recompiling.  If
>> it is with the patch, then try removing it and using it that way.
>>
>> To reverse a patch, you can use -R:
>>
>> patch -R < hybrid_remd.patch
>>
>> from AMBERHOME.
>>
>> Good luck,
>> Jason
>>
>> On Mon, Dec 20, 2010 at 12:30 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
>>
>>> 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
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> 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
>>>
>>
>>
>>
>> --
>> 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
>


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Received on Wed Dec 22 2010 - 01:30:03 PST
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