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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 12 2012 - 12:30:02 PDT
