Thanks for your reply, dac. But I'm still confused, isn't it the kinetic
energy get the kT/2 term?
I could understand the harmonic terms you are talking about, and that's
actually my concern, the result I got was the average through out the
simulation. I could agree that with higher temperature, the fluctuation of
bond angle and dihedral energy would be in a larger range. But since they
are harmonic, the average should still be the same, right? But the result
showed me the average was increasing linearly. Hope I made it clear...
-Binwu
On Mon, Aug 13, 2012 at 3:00 PM, <amber-request.ambermd.org> wrote:
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>
> Today's Topics:
>
> 1. Re: TI run energy does not conserve (Brian Radak)
> 2. Re: Problems parameterizing water/ZN active site with MKT++
> (Ben Roberts)
> 3. Production md (ariana karakutuk )
> 4. Re: Production md (case)
> 5. Internal energy linear increase with temperature (Binwu Zhao)
> 6. Re: Internal energy linear increase with temperature
> (David A Case)
> 7. Re: non integer charge in antechamber generated mol2 file (FyD)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 12 Aug 2012 15:14:34 -0400
> From: Brian Radak <radak004.umn.edu>
> Subject: Re: [AMBER] TI run energy does not conserve
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAJrka9wszeKt2Gq9SJhtnc5tQGuTQjN1MqG2ttzmpCVh76UMhQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> This is expected behavior. Pressure, volume, and density are only reported
> when barostatting is used. Likewise SCF energy is only reported when a
> QM/MM calculation is requested. The same goes for DV/DL which is only
> reported when a coupling of Hamiltonians is invoked using the TI code (you
> could also do this manually in the prmtop, but then DV/DL is not reported).
>
> I don't see anything obviously wrong with your simulations. What exactly is
> it that you are concerned about?
>
> On Fri, Aug 10, 2012 at 4:41 PM, <psu4.uic.edu> wrote:
>
> > Hi Brian,
> >
> > When I use "process_mdout.perl<
> > http://ambermd.org/tutorials/basic/tutorial1/files/process_mdout.perl>"
> > from the tutorial to process an output of my QMMM TI run
> > (123_QMMM-TI.out<
> > http://dl.dropbox.com/u/97270789/New%20folder/123_QMMM-TI.out>),
> > the energy and pressure seems no problem and can generate the correct
> > plots<http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png
> >.
> > However, the .DENSITY and .VOLUME are always empty.
> >
> > Here is my command.
> >
> > perl process_mdout.perl
> > 123_QMMM-TI.out<
> > http://dl.dropbox.com/u/97270789/New%20folder/123_QMMM-TI.out>
> >
> > The .out file is not a constant volume simulation. The density and the
> > volume info are recorded.
> >
> > The summary.VOLUME and summary.DENSITY will become like this (Here is the
> > .VOLUME. Only time info but not the volume info is processed.)
> >
> > Time
> > 100.250
> > 100.500
> > 100.750
> > 101.000
> > 101.250
> > 101.500
> > 101.750
> > 102.000
> > 102.250
> > 102.500
> > ..........
> >
> > However, for example, the summary.TEMP is normal.
> > Time Temp
> > 100.250 270.13
> > 100.500 286.46
> > 100.750 290.89
> > 101.000 296.04
> > 101.250 299.31
> > 101.500 299.82
> > 101.750 301.57
> > 102.000 301.14
> > 102.250 303.40
> > 102.500 298.73
> > 102.750 300.91
> > 103.000 300.91
> > 103.250 301.50
> > 103.500 300.79
> > 103.750 300.80
> > 104.000 300.16
> > 104.250 300.49
> > 104.500 301.66
> > 104.750 299.72
> > 105.000 299.12
> > ....... ......
> >
> > I also try to use
> > "process_mdout.perl<
> > http://ambermd.org/tutorials/basic/tutorial1/files/process_mdout.perl>"
> > to process an output file of a MM-MD run
> > (456_normal_MD.out<
> > http://dl.dropbox.com/u/97270789/New%20folder/456_normal_MD.out>)
> > and the volume/ density can be processed correctly.
> >
> > All the necessary files are provided in each link. I think the reason
> is
> > because in the QMMM-TI outputs, each recorded point contains two extra
> > terms:
> >
> > PM3ESCF= -205.6589
> > DV/DL = 0.0000
> >
> >
> > so the .perl script is confused. However, perl is not my strong
> subject
> > so could you give me some comments? Thank you.
> >
> > Best,
> > Henry
> >
> > On Fri, Aug 10, 2012 at 10:54 AM, Pin-Chih Su (Henry Su)) <
> > hs899886.gmail.com> wrote:
> >
> > > Brian,
> > >
> > > Thank you. I will keep trying and updating you the results.
> > >
> > > Cheers,
> > > Henry
> > >
> > > On Fri, Aug 10, 2012 at 8:20 AM, Brian Radak <radak004.umn.edu> wrote:
> > >
> > >> There have been a number of improvements to the QM/MM code between
> > AMBER11
> > >> and AMBER12 (the manuscript is nearing the end of preparation). With
> > >> limited information about you system, I could not tell you if any one
> of
> > >> them is responsible for the improved stability that you observe. I
> would
> > >> still, however, highly recommend that you continue using the new
> release
> > >> for QM/MM simulations as opposed to the old one.
> > >>
> > >> Regards,
> > >> Brian
> > >>
> > >> On Fri, Aug 10, 2012 at 3:16 AM, <psu4.uic.edu> wrote:
> > >>
> > >> > Brian,
> > >> >
> > >> > An Amber 12 test run in a 30 A box seems working fine. I will do
> > >> more
> > >> > runs to make sure it works fine. Since Amber 11 runs fail while an
> > >> Amber
> > >> > 12 run succeed, may I know if the Amber team has modified the
> related
> > >> codes
> > >> > in Amber 12 ?
> > >> >
> > >> > Thanks,
> > >> > Henry
> > >> >
> > >> > On Thu, Aug 9, 2012 at 9:30 AM, Brian Radak <radak004.umn.edu>
> wrote:
> > >> >
> > >> > > Henry,
> > >> > >
> > >> > > During QM/MM simulations with periodic boundaries, all atoms
> within
> > >> qmcut
> > >> > > (default is to match cut) of ANY qm atom are included in the
> direct
> > >> space
> > >> > > (and for QM/MM Lennard-Jones interactions). If that selection
> > reaches
> > >> > > outside the primary image, you will get the error you observed.
> > >> However,
> > >> > > the check is based on orthorhombic conditions and may fail
> > >> unnecessarily
> > >> > in
> > >> > > other boxes (Ross or Andreas, please correct me if this is wrong),
> > but
> > >> > this
> > >> > > is probably not a big deal in 90% of cases. You probably do just
> > need
> > >> a
> > >> > > bigger box, which is recommendable for TI calculations that change
> > >> charge
> > >> > > too. Another alternative is to use a smaller qmcut. In terms of
> > energy
> > >> > > conservation 8 works just about as well as 10 when using
> qmmm_switch
> > >> = 1,
> > >> > > especially when no d-orbitals are present. I've also observed some
> > >> > strange
> > >> > > simulations where an SCF instability causes the qm region to
> > "explode"
> > >> > and
> > >> > > trigger that error message.
> > >> > >
> > >> > > As for restraints, that could be a functional solution, although
> I'm
> > >> not
> > >> > > sure what you would restrain or if it would change the result of
> the
> > >> TI.
> > >> > My
> > >> > > general inclination is to avoid extra non-physically motivated
> > energy
> > >> > terms
> > >> > > whenever possible, but they can be pretty justifiable when the
> > >> > alternative
> > >> > > is catastrophic failure of the simulation.
> > >> > >
> > >> > > Regards,
> > >> > > Brian
> > >> > >
> > >> > > On Wed, Aug 8, 2012 at 6:02 PM, Pin-Chih Su (Henry Su) <
> > psu4.uic.edu>
> > >> > > wrote:
> > >> > >
> > >> > > > Brian,
> > >> > > >
> > >> > > > Thanks for your response. After I tried tempi= 100 or 150,
> the
> > >> > result
> > >> > > is
> > >> > > > identical. As you said, the energy is not conserved when enter
> the
> > >> QMMM
> > >> > > > production run and at the end of each stage, the energy will
> drop
> > as
> > >> > > > before. Please see the previous pictures as followed.
> > >> > > >
> > >> > > > *TI_energy<
> > >> > > >
> http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png>
> > >> > > > (**
> > >> >
> http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png**)*
> > >> > > > *TI_pressure<
> > >> > > >
> > http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png
> > >> >(
> > >> > > >
> > >> http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png)*
> > >> > > > *TI_temperature<
> > >> > > >
> > >> http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png
> > >> > >(
> > >> > > >
> > >> >
> > http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png)*
> > >> > > >
> > >> > > > So now I am trying to finish the whole TI cycles and do the
> > >> integral
> > >> > > to
> > >> > > > calculate the relative free energy between two ligands.
> However,
> > >> when
> > >> > I
> > >> > > am
> > >> > > > running the ligand-water (no protein) run, the following error
> > >> messages
> > >> > > > pops out in each production run.
> > >> > > >
> > >> > > > ****************************************************
> > >> > > > ERROR: QM region + cutoff larger than box dimension:
> > >> > > > QM-MM Cutoff = 10.0000
> > >> > > > Coord Lower Upper Size Radius of largest sphere
> > >> inside
> > >> > > unit
> > >> > > > cell
> > >> > > > X -12.960 12.051 25.011 14.723
> > >> > > > Y -12.337 12.147 24.484 14.723
> > >> > > > Z -14.754 14.694 29.448 14.723
> > >> > > > ****************************************************
> > >> > > > SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
> > >> > > > QM region + cutoff larger than box
> > >> > > > cannot continue, need larger box.
> > >> > > >
> > >> > > > I am aware there was the same issue in the other thread:
> > >> > > > http://archive.ambermd.org/201110/0139.html
> > >> > > >
> > >> > > > I can see from the MD movies that the ligand deviate from the
> > >> water
> > >> > box
> > >> > > > center significantly and thus the run fails. Thus, I have tried
> a
> > >> 30A
> > >> > > water
> > >> > > > box (the ligand itself is about 5A and the cutoff is 10A. So the
> > box
> > >> > size
> > >> > > > should be at least 10+10+5=25A) in Amber 11 but the same error
> > >> message
> > >> > > pops
> > >> > > > out. I am now trying in Amber 12 again. If it doesn't work, I
> > might
> > >> > try
> > >> > > a
> > >> > > > bigger box. But would you recommend if I restrain the ligand
> in a
> > >> > > > "ligand-water only" QMMM production run with a weak force so
> that
> > >> the
> > >> > > > ligand would not flow away? Will the restraint sabotage the
> > >> accuracy
> > >> > in
> > >> > > a
> > >> > > > TI run?
> > >> > > >
> > >> > > > The following is the proposed restraint script for
> convenience.
> > >> > > >
> > >> > > >
> ##################################################################
> > >> > > > mask0=':MAA.F14,CL17'
> > >> > > > mask1=
> > >> > > >
> > >> > > > for X in 1
> > >> > > >
> > >> > > > do
> > >> > > >
> > >> > > > ###################### minimization step
> > >> > ################################
> > >> > > >
> > >> > > > imin = 1,
> > >> > > > maxcyc = 2000,
> > >> > > > ntmin = 2,
> > >> > > > ntpr = 100,
> > >> > > > ntf = 2,
> > >> > > > ntc = 1, (I also tried ntc=2 here)
> > >> > > > ntb = 1,
> > >> > > > cut = 10.0,
> > >> > > > icfe = 1,
> > >> > > > clambda = 0.${X},
> > >> > > > ifsc=0,
> > >> > > > crgmask='${mask0}',
> > >> > > > &end
> > >> > > > ###########################Constant volume equilibrium to
> > >> equilibrate
> > >> > > > temperature ######################################
> > >> > > >
> > >> > > > imin = 0,
> > >> > > > irest = 0,
> > >> > > > ntx = 1,
> > >> > > > ntb = 1,
> > >> > > > cut = 10.0,
> > >> > > > ntr = 1,
> > >> > > > ntc = 2,
> > >> > > > ntf = 2,
> > >> > > > tempi = 0.0,
> > >> > > > temp0 = 300.0,
> > >> > > > ntt = 3,
> > >> > > > gamma_ln = 2.0,
> > >> > > > nstlim = 50000,
> > >> > > > dt = 0.001,
> > >> > > > ntpr = 250,
> > >> > > > ntwx = 250,
> > >> > > > ntwr = 2500,
> > >> > > > icfe = 1,
> > >> > > > clambda = 0.${X},
> > >> > > > ifsc=0,
> > >> > > > crgmask='${mask0}',
> > >> > > > */*
> > >> > > > *Keep the ligand fixed with weak restraints*
> > >> > > > *10.0*
> > >> > > > *.1-23
> > >> > > > *
> > >> > > > */*
> > >> > > >
> > >> > > > END
> > >> > > >
> > >> > > > ##################################### Constant Pressure
> > equilibrium
> > >> to
> > >> > > get
> > >> > > > a proper density #########################
> > >> > > > imin = 0,
> > >> > > > irest = 1,
> > >> > > > ntx = 7,
> > >> > > > ntb = 2,
> > >> > > > pres0 = 1.0,
> > >> > > > ntp = 1,
> > >> > > > taup = 2.0,
> > >> > > > cut = 10,
> > >> > > > ntr = 0,
> > >> > > > ntc = 2,
> > >> > > > ntf = 2,
> > >> > > > tempi = 300.0,
> > >> > > > temp0 = 300.0,
> > >> > > > ntt = 3,
> > >> > > > gamma_ln = 2.0,
> > >> > > > nstlim = 50000,
> > >> > > > dt = 0.001
> > >> > > > ntpr = 250,
> > >> > > > ntwx = 250,
> > >> > > > ntwr = 2500,
> > >> > > > icfe = 1,
> > >> > > > clambda = 0.${X},
> > >> > > > ifsc=0,
> > >> > > > crgmask='${mask0}',
> > >> > > > &end
> > >> > > > ############################QMMM production
> > >> > > > run###############################################
> > >> > > > imin = 0,
> > >> > > > ntx = 5,
> > >> > > > irest = 1,
> > >> > > > ntb = 2,
> > >> > > > ntp = 1,
> > >> > > > pres0 = 1.0,
> > >> > > > taup = 2.0,
> > >> > > > ntf = 1,
> > >> > > > ntc = 1,
> > >> > > > cut = 10.0,
> > >> > > > temp0 = 300.0,
> > >> > > > ntt = 3,
> > >> > > > gamma_ln = 2.0,
> > >> > > > nstlim = 50000,
> > >> > > > dt = 0.001,
> > >> > > > ntpr = 250,
> > >> > > > ntwr = 2500,
> > >> > > > ntwx = 250,
> > >> > > > icfe=1,
> > >> > > > clambda = 0.${X},
> > >> > > > ifsc=0,
> > >> > > > crgmask='${mask0}',
> > >> > > > ifqnt = 1
> > >> > > > /
> > >> > > > &qmmm
> > >> > > > iqmatoms= 1-23,
> > >> > > > qmchage=-1,
> > >> > > > qm_theory='PM3',
> > >> > > > qmshake=0,
> > >> > > > qm_ewald=1,
> > >> > > > qm_pme=1,
> > >> > > > * 10.0
> > >> > > > .1-23*
> > >> > > > /
> > >> > > > &end
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > >
> > >> >
> > >>
> >
> ############################################################################
> > >> > > >
> > >> > > >
> > >> > > > Cheers,
> > >> > > > Henry
> > >> > > >
> > >> > > >
> > >> > > > On Tue, Aug 7, 2012 at 9:09 AM, Brian Radak <radak004.umn.edu>
> > >> wrote:
> > >> > > >
> > >> > > > > Henry,
> > >> > > > >
> > >> > > > > I'm not an expert on ligand binding, but I believe the cycle
> in
> > >> the
> > >> > > > > tutorial will be compatible with QM/MM. The complication would
> > be
> > >> > that
> > >> > > > > there are different heats of formation for the ligands if they
> > >> differ
> > >> > > in
> > >> > > > > the number and kinds of atoms. This will appear as a (probably
> > >> > unknown)
> > >> > > > > constant shift in the *relative* free energy of transformation
> > >> > between
> > >> > > > > ligands because the potential energies are on different
> scales.
> > >> > > > >
> > >> > > > > However, if you calculate two relative free energies (one in
> > >> solution
> > >> > > and
> > >> > > > > one in the protein), then the shift will be the same in both
> > legs
> > >> and
> > >> > > > > formally cancel out when you calculate a relative binding free
> > >> > energy.
> > >> > > > You
> > >> > > > > can do the math yourself by assuming a constant in each QM
> > >> > Hamiltonian
> > >> > > > that
> > >> > > > > is only a function of the kinds of QM atoms and not their
> > >> > coordinates.
> > >> > > > The
> > >> > > > > constants will come out of the configuration integrals and
> thus
> > be
> > >> > > > additive
> > >> > > > > to the free energy.
> > >> > > > >
> > >> > > > > As for changing tempi, that may in fact be advantageous, but
> > will
> > >> not
> > >> > > > > change the fact that energy is not conserved. That behavior
> > should
> > >> > only
> > >> > > > be
> > >> > > > > desired/expected when ntt=0. Of course you will probably not
> get
> > >> > > > physically
> > >> > > > > meaningful results unless the system is first equilibrated
> near
> > >> the
> > >> > > > > temperature of interest (look up ensemble equivalence in the
> > book
> > >> by
> > >> > > > Allen
> > >> > > > > and Tildesley for example).
> > >> > > > >
> > >> > > > > Regards,
> > >> > > > > Brian
> > >> > > > >
> > >> > > > > On Mon, Aug 6, 2012 at 6:51 PM, Pin-Chih Su (Henry Su) <
> > >> psu4.uic.edu
> > >> > >
> > >> > > > > wrote:
> > >> > > > >
> > >> > > > > > Hi Brian,
> > >> > > > > >
> > >> > > > > > Thanks for the response. I am trying tempi = 100 & 150
> and
> > >> will
> > >> > > let
> > >> > > > > you
> > >> > > > > > know the result.
> > >> > > > > >
> > >> > > > > > Could you explain in more details about "how to carefully
> > >> > > calculated
> > >> > > > or
> > >> > > > > > canceled out byan appropriate thermodynamic cycle" to
> overcome
> > >> the
> > >> > > > subtle
> > >> > > > > > QMMM TI difficulties? If I follow and modify the protocol of
> > >> amber
> > >> > TI
> > >> > > > > > tutorial, <http://ambermd.org/tutorials/advanced/tutorial9/
> >
> > >> > will I
> > >> > > > > > overcome the subtle QMMM TI difficulty? Or there are
> something
> > >> > > > important
> > >> > > > > > tips not mentioned in the tutorial?
> > >> > > > > >
> > >> > > > > > When visualized the QMMM TI trajectory, I don't see weird
> > >> > points.
> > >> > > > > The
> > >> > > > > > ligand still binds to the protein active site with normal
> > >> > > fluctuation;
> > >> > > > no
> > >> > > > > > blow up. The following is the RMSD v.s. time plot of the
> 100
> > >> ps
> > >> > > > > > production run in step 3, V0 group.
> > >> > > > > >
> > >> > > > > > http://i1076.photobucket.com/albums/w454/happypsu4/RMSD.jpg
> > >> > > > > >
> > >> > > > > > Here is my RMSD script
> > >> > > > > >
> > >> > > > > > ######################################
> > >> > > > > > cat << EOF > AAA.calc_rms
> > >> > > > > >
> > >> > > > > > trajin BBB.mdcrd
> > >> > > > > >
> > >> > > > > > reference C.inpcrd
> > >> > > > > >
> > >> > > > > > rms reference mass out AAA.rms .N,CA,C time 0.5
> > >> > > > > >
> > >> > > > > > EOF
> > >> > > > > >
> > >> > > > > > $AMBERHOME/bin/ptraj C.prmtop < AAA.calc_rms
> > >> > > > > > ###############################################
> > >> > > > > >
> > >> > > > > > Please let me know if any comment.
> > >> > > > > >
> > >> > > > > > Many thanks,
> > >> > > > > > Henry
> > >> > > > > >
> > >> > > > > > On Fri, Aug 3, 2012 at 1:44 PM, Brian Radak <
> radak004.umn.edu
> > >
> > >> > > wrote:
> > >> > > > > >
> > >> > > > > > > Hi Henry,
> > >> > > > > > >
> > >> > > > > > > You appear to be running thermostatted MD (ntt != 1 and
> > >> gamma_ln
> > >> > >
> > >> > > > 0),
> > >> > > > > in
> > >> > > > > > > which case energy shouldn't be conserved, especially when
> > you
> > >> set
> > >> > > > > tempi =
> > >> > > > > > > 0., as the system quickly converts potential energy into
> > >> kinetic
> > >> > > > > energy.
> > >> > > > > > > You might consider speeding that up by setting tempi > 0
> or
> > >> using
> > >> > > > > various
> > >> > > > > > > heating protocols.
> > >> > > > > > >
> > >> > > > > > > As for QM/MM, I believe it is quite normal for the energy
> to
> > >> jump
> > >> > > as
> > >> > > > > the
> > >> > > > > > QM
> > >> > > > > > > code includes atomic heats of formation and therefore has
> a
> > >> > > different
> > >> > > > > > zero
> > >> > > > > > > of potential energy. This is a subtle difficulty in
> > >> performing TI
> > >> > > > with
> > >> > > > > > > QM/MM because the zero of energy will be an offset in any
> > free
> > >> > > > energies
> > >> > > > > > > that you compute and must either be carefully calculated
> or
> > >> > > canceled
> > >> > > > > out
> > >> > > > > > by
> > >> > > > > > > an appropriate thermodynamic cycle.
> > >> > > > > > >
> > >> > > > > > > Are your dynamics unstable? Relatively large changes in
> > energy
> > >> > > during
> > >> > > > > > > equilibration are not necessarily cause for concern unless
> > you
> > >> > are
> > >> > > > > > getting
> > >> > > > > > > vlimit or SHAKE errors.
> > >> > > > > > >
> > >> > > > > > > Regards,
> > >> > > > > > > Brian
> > >> > > > > > >
> > >> > > > > > > On Fri, Aug 3, 2012 at 1:44 PM, Pin-Chih Su (Henry Su) <
> > >> > > psu4.uic.edu
> > >> > > > >
> > >> > > > > > > wrote:
> > >> > > > > > >
> > >> > > > > > > > Dear Amber,
> > >> > > > > > > >
> > >> > > > > > > > When I run a TI job, the energy doesn't seem to
> > conserve
> > >> in
> > >> > > each
> > >> > > > > > > clambda
> > >> > > > > > > > step in no matter step 1, step 2 (soft core potential
> > step)
> > >> and
> > >> > > > step
> > >> > > > > 3.
> > >> > > > > > > > The total energy always drops significantly at the
> > >> beginning
> > >> > of
> > >> > > > each
> > >> > > > > > > stage
> > >> > > > > > > > (minimization, constant volume equilibrium, constant
> > >> > > > > > > > pressure equilibrium and production run). Moreover, when
> > MD
> > >> > > enters
> > >> > > > > > into a
> > >> > > > > > > > QMMM production run, the total energy will drop again
> and
> > >> then
> > >> > > > reach
> > >> > > > > a
> > >> > > > > > > > higher value than the total energy of minimization and
> > >> > > equilibrium.
> > >> > > > > > > Please
> > >> > > > > > > > see the following Xmgrace figures for more details.
> > >> > > > > > > >
> > >> > > > > > > > *TI_energy<
> > >> > > > > > > >
> > >> > http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png
> > >> > > >
> > >> > > > > > > > (**
> > >> > > > > >
> > >> >
> http://i1076.photobucket.com/albums/w454/happypsu4/TI_energy.png**)*
> > >> > > > > > > > *TI_pressure<
> > >> > > > > > > >
> > >> > >
> http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png
> > >> > > > >(
> > >> > > > > > > >
> > >> > > >
> > >> http://i1076.photobucket.com/albums/w454/happypsu4/TI_pressure.png)*
> > >> > > > > > > > *TI_temperature<
> > >> > > > > > > >
> > >> > > > >
> > >> >
> http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png
> > >> > > > > > >(
> > >> > > > > > > >
> > >> > > > > >
> > >> > > >
> > >> >
> > http://i1076.photobucket.com/albums/w454/happypsu4/TI_temperature.png)*
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > > The following is my Amber TI script in step 1 (to
> > >> simplify, I
> > >> > > > just
> > >> > > > > > show
> > >> > > > > > > > half of the script, as in a group ):
> > >> > > > > > > >
> > >> > > > > > > > mask0=':MAA.F14,CL17'
> > >> > > > > > > > mask1=
> > >> > > > > > > >
> > >> > > > > > > > for X in 1,2,3
> > >> > > > > > > >
> > >> > > > > > > > do
> > >> > > > > > > >
> > >> > > > > > > > ###################### minimization step
> > >> > > > > > ################################
> > >> > > > > > > >
> > >> > > > > > > > imin = 1,
> > >> > > > > > > > maxcyc = 2000,
> > >> > > > > > > > ntmin = 2,
> > >> > > > > > > > ntpr = 100,
> > >> > > > > > > > ntf = 2,
> > >> > > > > > > > ntc = 1, (I also tried ntc=2 here)
> > >> > > > > > > > ntb = 1,
> > >> > > > > > > > cut = 10.0,
> > >> > > > > > > > icfe = 1,
> > >> > > > > > > > clambda = 0.${X},
> > >> > > > > > > > ifsc=0,
> > >> > > > > > > > crgmask='${mask0}',
> > >> > > > > > > > &end
> > >> > > > > > > > ###########################Constant volume equilibrium
> to
> > >> > > > equilibrate
> > >> > > > > > > > temperature ######################################
> > >> > > > > > > >
> > >> > > > > > > > imin = 0,
> > >> > > > > > > > irest = 0,
> > >> > > > > > > > ntx = 1,
> > >> > > > > > > > ntb = 1,
> > >> > > > > > > > cut = 10.0,
> > >> > > > > > > > ntr = 1,
> > >> > > > > > > > ntc = 2,
> > >> > > > > > > > ntf = 2,
> > >> > > > > > > > tempi = 0.0,
> > >> > > > > > > > temp0 = 300.0,
> > >> > > > > > > > ntt = 3,
> > >> > > > > > > > gamma_ln = 2.0,
> > >> > > > > > > > nstlim = 50000,
> > >> > > > > > > > dt = 0.001,
> > >> > > > > > > > ntpr = 250,
> > >> > > > > > > > ntwx = 250,
> > >> > > > > > > > ntwr = 2500,
> > >> > > > > > > > icfe = 1,
> > >> > > > > > > > clambda = 0.${X},
> > >> > > > > > > > ifsc=0,
> > >> > > > > > > > crgmask='${mask0}',
> > >> > > > > > > > /
> > >> > > > > > > > Keep the Protein fixed with weak restraints
> > >> > > > > > > > 10.0
> > >> > > > > > > > RES 1 258
> > >> > > > > > > > /
> > >> > > > > > > >
> > >> > > > > > > > END
> > >> > > > > > > >
> > >> > > > > > > > ##################################### Constant Pressure
> > >> > > equilibrium
> > >> > > > > to
> > >> > > > > > > get
> > >> > > > > > > > a proper density #########################
> > >> > > > > > > > imin = 0,
> > >> > > > > > > > irest = 1,
> > >> > > > > > > > ntx = 7,
> > >> > > > > > > > ntb = 2,
> > >> > > > > > > > pres0 = 1.0,
> > >> > > > > > > > ntp = 1,
> > >> > > > > > > > taup = 2.0,
> > >> > > > > > > > cut = 10,
> > >> > > > > > > > ntr = 0,
> > >> > > > > > > > ntc = 2,
> > >> > > > > > > > ntf = 2,
> > >> > > > > > > > tempi = 300.0,
> > >> > > > > > > > temp0 = 300.0,
> > >> > > > > > > > ntt = 3,
> > >> > > > > > > > gamma_ln = 2.0,
> > >> > > > > > > > nstlim = 50000,
> > >> > > > > > > > dt = 0.001
> > >> > > > > > > > ntpr = 250,
> > >> > > > > > > > ntwx = 250,
> > >> > > > > > > > ntwr = 2500,
> > >> > > > > > > > icfe = 1,
> > >> > > > > > > > clambda = 0.${X},
> > >> > > > > > > > ifsc=0,
> > >> > > > > > > > crgmask='${mask0}',
> > >> > > > > > > > &end
> > >> > > > > > > > ############################QMMM production
> > >> > > > > > > > run###############################################
> > >> > > > > > > > imin = 0,
> > >> > > > > > > > ntx = 5,
> > >> > > > > > > > irest = 1,
> > >> > > > > > > > ntb = 2,
> > >> > > > > > > > ntp = 1,
> > >> > > > > > > > pres0 = 1.0,
> > >> > > > > > > > taup = 2.0,
> > >> > > > > > > > ntf = 1,
> > >> > > > > > > > ntc = 1,
> > >> > > > > > > > cut = 10.0,
> > >> > > > > > > > temp0 = 300.0,
> > >> > > > > > > > ntt = 3,
> > >> > > > > > > > gamma_ln = 2.0,
> > >> > > > > > > > nstlim = 50000,
> > >> > > > > > > > dt = 0.001,
> > >> > > > > > > > ntpr = 250,
> > >> > > > > > > > ntwr = 2500,
> > >> > > > > > > > ntwx = 250,
> > >> > > > > > > > icfe=1,
> > >> > > > > > > > clambda = 0.${X},
> > >> > > > > > > > ifsc=0,
> > >> > > > > > > > crgmask='${mask0}',
> > >> > > > > > > > ifqnt = 1
> > >> > > > > > > > /
> > >> > > > > > > > &qmmm
> > >> > > > > > > > iqmatoms= 3868,3869,3870,3871,3872,
> > >> > > > > > > > 3873,3874,3875,3876,3877,
> > >> > > > > > > > 3878,3879,3880,3881,3882,
> > >> > > > > > > > 3883,3884,3885,3886,3887,
> > >> > > > > > > > 3888,3889,3890,1395,1394,
> > >> > > > > > > > 1396,1398,1399,2328,2327,
> > >> > > > > > > > 3833,3834,3835,3836,3837,
> > >> > > > > > > > 3838,3839,3840,3841,3862,
> > >> > > > > > > > 3863,3864,3865,3866,3867,
> > >> > > > > > > > qmchage=-1,
> > >> > > > > > > > qm_theory='PM3',
> > >> > > > > > > > qmshake=0,
> > >> > > > > > > > qm_ewald=1,
> > >> > > > > > > > qm_pme=1,
> > >> > > > > > > > /
> > >> > > > > > > > &end
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > > >
> > >> > > > > > >
> > >> > > > > >
> > >> > > > >
> > >> > > >
> > >> > >
> > >> >
> > >>
> >
> ############################################################################
> > >> > > > > > > >
> > >> > > > > > > > I have tried
> > >> > > > > > > >
> > >> > > > > > > > a. turn off QMMM. Or keep QMMM but with qmshake=1,. The
> > same
> > >> > > issue
> > >> > > > > > > > b. Run in both Amber 11 & 12, The same issue
> > >> > > > > > > > c. Turn on / off SHAKE. The same issue.
> > >> > > > > > > > d. Turn off Langevin Dynamic. The same issue
> > >> > > > > > > > e. Switch to Andersen temperature control. The same
> issue.
> > >> > > > > > > > f. Prepare new .prmtop and .inpcrd files and run again.
> > The
> > >> > same
> > >> > > > > issue
> > >> > > > > > > > g. I have set ntpr=1 and check all the .out files by
> "gvim
> > >> -d"
> > >> > > and
> > >> > > > > > total
> > >> > > > > > > > energies, temperature, pressure and all the MM
> components
> > >> are
> > >> > the
> > >> > > > > same
> > >> > > > > > in
> > >> > > > > > > > the same group file.
> > >> > > > > > > > h. The restart files from V0 to V1 are identical.
> > >> > > > > > > >
> > >> > > > > > > > I only tried 9 windows so far.
> > >> > > > > > > > clambda = 0.${X}, for X in 1 2 3 4 5 6 7 8 9
> > >> > > > > > > > But I guess number of windows is not the issue here.
> > >> > > > > > > >
> > >> > > > > > > > Please let me know if any comment. Many comments.
> > >> > > > > > > >
> > >> > > > > > > > Henry
> > >> > > > > > > > _______________________________________________
> > >> > > > > > > > AMBER mailing list
> > >> > > > > > > > AMBER.ambermd.org
> > >> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > > > >
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > > --
> > >> > > > > > > ================================ Current Address
> > >> > > > > =======================
> > >> > > > > > > Brian Radak :
> > >> > > > BioMaPS
> > >> > > > > > > Institute for Quantitative Biology
> > >> > > > > > > PhD candidate - York Research Group : Rutgers,
> > The
> > >> > State
> > >> > > > > > > University of New Jersey
> > >> > > > > > > University of Minnesota - Twin Cities :
> Center
> > >> for
> > >> > > > > > Integrative
> > >> > > > > > > Proteomics Room 308
> > >> > > > > > > Graduate Program in Chemical Physics : 174
> > >> Frelinghuysen
> > >> > > > Road,
> > >> > > > > > > Department of Chemistry :
> > >> > Piscataway,
> > >> > > > NJ
> > >> > > > > > > 08854-8066
> > >> > > > > > > radak004.umn.edu :
> > >> > > > > > > radakb.biomaps.rutgers.edu
> > >> > > > > > >
> > >> > >
> ====================================================================
> > >> > > > > > > Sorry for the multiple e-mail addresses, just use the
> > >> institute
> > >> > > > > > appropriate
> > >> > > > > > > address.
> > >> > > > > > > _______________________________________________
> > >> > > > > > > AMBER mailing list
> > >> > > > > > > AMBER.ambermd.org
> > >> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > > >
> > >> > > > > >
> > >> > > > > >
> > >> > > > > >
> > >> > > > > > --
> > >> > > > > >
> > >> > > > > > Pin-Chih Su (Henry Su)
> > >> > > > > >
> > >> > > > > > Graduate Student
> > >> > > > > >
> > >> > > > > > Center for Pharmaceutical Biotechnology (MC 870)
> > >> > > > > >
> > >> > > > > > College of Pharmacy, University of Illinois at Chicago
> > >> > > > > >
> > >> > > > > > 900 South Ashland Avenue, Room 1052
> > >> > > > > >
> > >> > > > > > Chicago, IL 60607-7173
> > >> > > > > >
> > >> > > > > > office 312-996-5388
> > >> > > > > >
> > >> > > > > > fax 312-413-9303
> > >> > > > > > _______________________________________________
> > >> > > > > > AMBER mailing list
> > >> > > > > > AMBER.ambermd.org
> > >> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > >
> > >> > > > > --
> > >> > > > > ================================ Current Address
> > >> > > =======================
> > >> > > > > Brian Radak :
> > >> > BioMaPS
> > >> > > > > Institute for Quantitative Biology
> > >> > > > > PhD candidate - York Research Group : Rutgers, The
> > >> State
> > >> > > > > University of New Jersey
> > >> > > > > University of Minnesota - Twin Cities : Center
> for
> > >> > > > Integrative
> > >> > > > > Proteomics Room 308
> > >> > > > > Graduate Program in Chemical Physics : 174
> > Frelinghuysen
> > >> > Road,
> > >> > > > > Department of Chemistry :
> > >> Piscataway,
> > >> > NJ
> > >> > > > > 08854-8066
> > >> > > > > radak004.umn.edu :
> > >> > > > > radakb.biomaps.rutgers.edu
> > >> > > > >
> > >> ====================================================================
> > >> > > > > Sorry for the multiple e-mail addresses, just use the
> institute
> > >> > > > appropriate
> > >> > > > > address.
> > >> > > > > _______________________________________________
> > >> > > > > AMBER mailing list
> > >> > > > > AMBER.ambermd.org
> > >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > > >
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > > --
> > >> > > >
> > >> > > > Pin-Chih Su (Henry Su)
> > >> > > >
> > >> > > > Graduate Student
> > >> > > >
> > >> > > > Center for Pharmaceutical Biotechnology (MC 870)
> > >> > > >
> > >> > > > College of Pharmacy, University of Illinois at Chicago
> > >> > > >
> > >> > > > 900 South Ashland Avenue, Room 1052
> > >> > > >
> > >> > > > Chicago, IL 60607-7173
> > >> > > >
> > >> > > > office 312-996-5388
> > >> > > >
> > >> > > > fax 312-413-9303
> > >> > > > _______________________________________________
> > >> > > > AMBER mailing list
> > >> > > > AMBER.ambermd.org
> > >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> > > >
> > >> > >
> > >> > >
> > >> > >
> > >> > > --
> > >> > > ================================ Current Address
> > >> =======================
> > >> > > Brian Radak :
> > BioMaPS
> > >> > > Institute for Quantitative Biology
> > >> > > PhD candidate - York Research Group : Rutgers, The
> State
> > >> > > University of New Jersey
> > >> > > University of Minnesota - Twin Cities : Center for
> > >> > Integrative
> > >> > > Proteomics Room 308
> > >> > > Graduate Program in Chemical Physics : 174 Frelinghuysen
> > >> Road,
> > >> > > Department of Chemistry :
> Piscataway,
> > NJ
> > >> > > 08854-8066
> > >> > > radak004.umn.edu :
> > >> > > radakb.biomaps.rutgers.edu
> > >> > >
> ====================================================================
> > >> > > Sorry for the multiple e-mail addresses, just use the institute
> > >> > appropriate
> > >> > > address.
> > >> > > _______________________________________________
> > >> > > 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
> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> ================================ Current Address
> =======================
> > >> Brian Radak : BioMaPS
> > >> Institute for Quantitative Biology
> > >> PhD candidate - York Research Group : Rutgers, The State
> > >> University of New Jersey
> > >> University of Minnesota - Twin Cities : Center for
> > >> Integrative
> > >> Proteomics Room 308
> > >> Graduate Program in Chemical Physics : 174 Frelinghuysen
> Road,
> > >> Department of Chemistry : Piscataway, NJ
> > >> 08854-8066
> > >> radak004.umn.edu :
> > >> radakb.biomaps.rutgers.edu
> > >> ====================================================================
> > >> Sorry for the multiple e-mail addresses, just use the institute
> > >> appropriate
> > >> address.
> > >> _______________________________________________
> > >> 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
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 13 Aug 2012 20:19:10 +1200
> From: Ben Roberts <ben.roberts.geek.nz>
> Subject: Re: [AMBER] Problems parameterizing water/ZN active site with
> MKT++
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <C1AC28DC-9804-4EF3-94EE-D234A634A6CF.roberts.geek.nz>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Fabr?cio,
>
> Do you think you could send me your BCL scripts, input PDB file (cleaned
> up and ready for MTK++), and Gaussian outputs? Or, if they're too big to
> email, could you put them on a web server so I can download them?
>
> Cheers,
> Ben
>
> On 12/08/2012, at 9:48 PM, Ben Roberts wrote:
>
> > Hi Fabr?cio,
> >
> > No, I've been a bit busy the last week. I'll try to look into it
> shortly, maybe tomorrow evening.
> >
> > Cheers,
> > Ben
> >
> > On 11/08/2012, at 12:47 AM, Fabr?cio Bracht wrote:
> >
> >> Hi Ben. Any progress on the problem yet?
> >> Thank you
> >> Fabr?cio
> >>
> >> 2012/8/5 Ben Roberts <ben.roberts.geek.nz>:
> >>> Righto. I'll have a look at the docs tonight and see if I can recall
> the procedure. Then I'll ask for whatever I think I need.
> >>>
> >>> Cheers,
> >>> Ben
> >>>
> >>> On 6/08/2012, at 2:39 AM, Fabr?cio Bracht wrote:
> >>>
> >>>> Hi Ben. No, I did pretty much the same thing described on the MTK++
> >>>> manual standard procedure. I did the same thing for parameterizing the
> >>>> same active site, but instead of a water molecule I had an hydroxyl
> >>>> ion. The procedure with the hydroxyl ion worked like a clock. If you
> >>>> like, I can send you some of the files. Just tell me if you need
> >>>> anything.
> >>>> Fabr?cio Bracht
> >>>>
> >>>> 2012/8/5 Ben Roberts <ben.roberts.geek.nz>:
> >>>>> Hi Fabr?cio,
> >>>>>
> >>>>> Is it exactly 0 on the Zn? That does sound very suspicious.
> Unfortunately, the MTK++ steps are a fairly complicated procedure. Did you
> deviate from the standard procedure for the latter part of the MTK++
> parameterisation in any way?
> >>>>>
> >>>>> Cheers,
> >>>>> Ben
> >>>>>
> >>>>> On 1/08/2012, at 7:36 AM, Fabr?cio Bracht wrote:
> >>>>>
> >>>>>> Hello. After a long discussion on the parameterization of an active
> >>>>>> site containing zinc and a hydroxyl molecule
> >>>>>> (http://archive.ambermd.org/201205/0452.html), I've started
> >>>>>> parameterization of the same active site, but this time with the
> water
> >>>>>> molecule instead of a hydroxyl bound to zinc. Everything seems to go
> >>>>>> ok, including gaussian calculations, but once I get to the creation
> of
> >>>>>> the xml files and after that, to the creation of the prep file, I
> see
> >>>>>> that the charge distribution is nothing like I would expect. The
> >>>>>> procedure places 0 charge on the zinc atom, 0 charge on the oxygen
> >>>>>> (water) atom and very small charges on the water hydrogen atoms.
> >>>>>> Furthermore, I've checked with the ZAFF xml files distributed with
> the
> >>>>>> original paper, and the charges are very different than the ones
> they
> >>>>>> got. The charges are very different than the ones on the ESP fit in
> >>>>>> the gaussian output file. Could it be something with the espgen or
> >>>>>> respgen routines as written in the getcharges.sh file?
> >>>>>> The ESP CHARGES calculated by gaussian are : (O, H and H are the
> atoms
> >>>>>> that form the water molecule).
> >>>>>> Zn 0.85630372D+00
> >>>>>> O -0.94007825D+00
> >>>>>> H 0.50049376D+00
> >>>>>> H 0.41322947D+00
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>
> >>> --
> >>> For greater security, I support S/MIME encryption.
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> > --
> > For greater security, I support S/MIME encryption.
> >
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 13 Aug 2012 10:06:04 +0000
> From: "ariana karakutuk " <arianakarakutuk.hotmail.com>
> Subject: [AMBER] Production md
> To: "amber.ambermd.org " <amber.ambermd.org>
> Message-ID: <DUB103-ds30F141404C093D6AA7528B6B00.phx.gbl>
> Content-Type: text/plain; charset="iso-8859-9"
>
> Hello,
> I'm new in AMBER. I'm trying to fold the missing sequences of a protein,
> but in the result the molecules diffuse very far away from each other.
> Here's my input file:
>
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=250000, dt=0.002,
> ntc=2, ntf=2,
> ntt=1, tautp=0.5,
> tempi=325.0, temp0=325.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=1,
> cut=999., rgbmax=999.
> /
> Hold the protein fixed
> 100.0
> RES 1 8 27 105
> END
> END
>
> thank you..
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 13 Aug 2012 08:35:01 -0400
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Production md
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120813123501.GC50238.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Aug 13, 2012, ariana karakutuk wrote:
>
> > I'm new in AMBER. I'm trying to fold the missing sequences of a protein,
> > but in the result the molecules diffuse very far away from each
> > other. Here's my input file:
>
> Please describe your calculation in more detail. It looks like maybe(??)
> you have (experimental?) coordinates for residues 1-8 and 27-105, but not
> for
> residues 9-26. But you don't say how you prepared the initial coordinates,
> nor what the "molecules" are that diffuse far away from each other. It's
> hard
> to give any good advice without more idea of what you did.
>
> [Note: if you do have a big stretch of missing residues in a single
> polypeptide chain, Amber is not a very good program to estimate where the
> missing pieces are. In this case, you would probably want a homology
> modeling
> program of some sort.]
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 13 Aug 2012 11:01:19 -0400
> From: Binwu Zhao <bzhao.ncsu.edu>
> Subject: [AMBER] Internal energy linear increase with temperature
> To: amber.ambermd.org
> Message-ID:
> <CABNUZL1MRSrXL1ikb_-6NgDjK=f-V7ttj_mthZij5Kh_rw=
> NLw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber Users:
>
> I've encountered some problems with the internal energy calculated by
> MMPBSA.pl, I only have one chain in the system, and I removed water before
> the calculation. But the result showed that the internal energy is
> increasing linearly along with the temperature, I separated the bonded
> energy, angle energy and dihedral energy but found out they were all
> increasing linearly with the temperature.
> The data I used was the average through out the total simulation time. I
> can understand that with higher temperature, the internal energy might
> be fluctuating in a larger range, but the average is also increasing
> linearly? This increasing made the total energy of the chain a positive
> number, but in fact the chain is collapsing. Which is very confusing to
> me...Is it the way that amber calculates the energy? Force field?
> Hope you guys could help me here, any suggestions would be really
> appreciative. Thanks!!!
>
> -Binwu
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 13 Aug 2012 11:16:19 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Internal energy linear increase with temperature
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120813151619.GB19122.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Aug 13, 2012, Binwu Zhao wrote:
> >
> > But the result showed that the internal energy is
> > increasing linearly along with the temperature...
>
> Sounds correct to me. In classical statistical mechanics, each squared
> term
> in the Hamiltonian gets kT/2 of energy. Since the internal energy is
> dominated by harmonic bond and angle terms, (and even the dihedrals are
> often
> approximately harmonic near their minima), you should expect the internal
> energy to be proportional to temperature.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 13 Aug 2012 18:35:31 +0200
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] non integer charge in antechamber generated mol2
> file
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120813183531.vppj19j8ggwwkg0g.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Raik,
>
> > In this case though, I guess there is nothing wrong with my workaround
> > of simply scaling all the partial charges in the mol2 by a tiny bit
> > such that the sum is perfectly integer, or is there?
>
> You can indeed modify by hand the charge values in the mol2 file in
> agreement with chemical equivalencing; except that the program you use
> should provide you a total charge value with correct chemical
> equivalencing (for MD simulations) with rounding off errors (or
> without rounding off errors). If not this might reflect a more
> important problem...
>
> > That's what the
> > quick and dirty python script is doing (attached to my previous mail).
>
> Many people 'arrange' by hand charge values - in particular, when one
> wants to generate charge values for a molecular fragments. Personally,
> I vote against this type of approach.
>
> The R.E.D. program has been designed to rigorously derive MEP (RESP
> and ESP) based charges for whole molecules _and_ molecular fragments
> (see tutorials at http://q4md-forcefieldtools.org/Tutorial/); avoiding
> quick and dirty work after charge derivation ;-) All the parameters
> that affect MEP based charge values (when using a fixed charge model
> so far) are fully controlled, were extensively tested and are in
> agreement with the original publications...
> See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
> & http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/#S7title
> the "Charge reproducibility" section...
>
> regards, Francois
>
>
> > On Thu, Aug 9, 2012 at 11:53 AM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >> Dear Raik,
> >>
> >> When one derives charge values for a whole molecule or even for a
> >> molecular fragment rounding off errors are always generated; however,
> >> these rounding off errors are related to the number of digits after
> >> the decimal point chosen by the user for the charge values.
> >>
> >> Thus for a whole molecule, if four digits are requested one ends up
> >> with charge values such as:
> >> +/- X.000Y; X the wanted integer value; Y the rounding off error
> >> generally, Y has a max. value of around 5-7.
> >>
> >> In the case you presented: '-0.996001' there are 6 digits after the
> >> decimal points. So the rounding off error should have the following
> >> shape: '-0.99999Y'
> >>
> >> My feeling is that the difference between -1.000000 (the value you
> >> want) and -0.996001 is _not_ a rounding off error... (& I think this
> >> problem is known; and Antechamber has used many different programs
> >> with or without correct charge equivalencing in the past; so this is
> >> 'normal' (personally, I do not think this is 'normal') the charges
> >> generated by Amber?->12/Antechamber are different).
> >>
> >> If you do want to derive a correct integer value for your molecule,
> >> you could download the R.E.D. tools or freely use R.E.D. Server to
> >> generate the mol2 file for your molecule. The last version of R.E.D.
> >> and R.E.D. Server do incorporate a new algorithm for automatically
> >> correcting (real) rounding off errors at a chosen accuracy in
> >> agreement with chemical equivalencing. Thus, instead of obtaining
> >> -0.99999Y (which is correct compared to -0.996001) you will get
> >> -1.000000 (or -1.0000 instead of -0.999Y; this accuracy was that
> >> originally used).
> >>
> >> I hope this helps.
> >>
> >> regards, Francois
> >>
> >>
> >>> I have used antechamber and parmchk to create a mol2 and frcmod file
> >>> for a small organic protein ligand with a charge of -1. The original
> >>> coordinates were extracted from the PDB and hydrogens added with
> >>> Chimera.
> >>>
> >>> I then run:
> >>> antechamber -i in.pdb -fi pdb -o out.mol2 -fo mol2 -c bcc -nc -1&
> >>> followed by:
> >>> parmchk -i *mol2 -f mol2 -o out.frcmod
> >>>
> >>> All seems to have worked and sqm.out reports a total charge of:
> >>>> Total Mulliken Charge = -1.000
> >>>
> >>> In reality though, the charges of the mol2 file add up to:
> >>> -0.996001
> >>> (In fact, the charges in the output mol2 are different from the
> sqm.out.)
> >>>
> >>> This is enough to make the charge neutralization in tleap fail, i.e.
> >>> one ion is added too little, and the overall charge of the system
> >>> cannot be brought to a clean 0.
> >>>
> >>> I see the same thing happening on two different machines (Ubuntu 12.04
> >>> 64bit), with a fresh Amber/AmberTools12 compilation (default gnu
> >>> compilers), all patches applied.
> >>>
> >>> Funny enough, if I generate a mol2 with Chimera (which is using
> >>> antechamber from amber version 11) the charges sum up well and the
> >>> problem doesn't seem to exist. But the resulting charges are quite
> >>> different in detail and I want to stick to Amber 12.
> >>>
> >>> I guess a workaround will be to write a simple script that scales all
> >>> partial charges to enforce a -1.0000 overall charge. Is there any more
> >>> general solution?
>
>
>
>
>
>
> ------------------------------
>
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>
> End of AMBER Digest, Vol 243, Issue 1
> *************************************
>
--
Binwu Zhao
Dept of Chemical and Biomolecular Engineerig
NCSU
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Received on Mon Aug 20 2012 - 13:00:03 PDT
