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
Received on Fri Aug 10 2012 - 14:00:06 PDT
