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

From: Bongkeun Kim <bkim.chem.ucsb.edu>
Date: Wed, 22 Dec 2010 11:21:03 -0800

Thank you for your patch.
But it seems like it still has a problem.
Please take a look following output.
Bongkeun Kim
.@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
=================HYBRID REMD: energy calc for exch 1=================
HYBRID REMD: Stripping waters
wrapping first mol.: 83.13530 0.00000 41.15202
wrapping first mol.: 83.13530 81.46523 41.15202
HYBRID REMD: New natom= 4820
HYBRID REMD: New ref 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 =
18358499.0386
  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 =
17751963.4196
  EAMBER (non-restraint) = 606535.6191
  TEMP0 = 285.1000 REPNUM = 1 EXCHANGE# =
         0
   
------------------------------------------------------------------------------

HYBRID REMD: myEptot= 18358499.0386 myTargetTemp= 285.10
HYBRID REMD: Restoring...
=========================END HYBRID REMD energy calc.=========================
REMD: myEptot= 18358499.0386 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= 1.33 Success= T
========================END REMD EXCHANGE CALCULATION========================
REMD: checking to see if bath T has changed: 285.10->501.00
REMD: scaling velocities by 1.326 to match new bath T 501.000
| # 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.

.@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

Quoting Daniel Roe <daniel.r.roe.gmail.com>:

> 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 - 11:30:03 PST
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