Found out what the problem was. When creating the prmtop files, the order
of the atoms was different. Fixed it already.
Thank you again
Fabrício
2013/2/4 Brian Radak <radak004.umn.edu>
> What do your input files and group file look like? Also, if you are using
> the normal TI code you must provide prmtop files with identical numbers of
> atoms.
>
> On Mon, Feb 4, 2013 at 2:21 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
>
> > Ok. I removed the softcore potential and tried to run the simulation for
> > lambda 1.0 but the simulation crashes before it even starts. The error
> >
> > Running multisander version of sander Amber12
> > Total processors = 2
> > Number of groups = 2
> >
> > [woodstock:18042] *** An error occurred in MPI_Sendrecv
> > [woodstock:18042] *** on communicator MPI COMMUNICATOR 4 SPLIT FROM 0
> > [woodstock:18042] *** MPI_ERR_TRUNCATE: message truncated
> > [woodstock:18042] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> >
> --------------------------------------------------------------------------
> > mpirun has exited due to process rank 1 with PID 18042 on
> > node woodstock exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> > Comes out on screen. The command given was
> > mpirun -np 2 sander.MPI -ng 2 -groupfile group_heat1
> >
> > Am I doing something wrong here?
> >
> > 2013/2/4 Brian Radak <radak004.umn.edu>
> >
> > > Fabricio,
> > >
> > > Unfortunately, I have no idea if the softcore potential code is
> > compatible
> > > with the QM/MM code. I believe the topology information is handled in a
> > > slightly unusual way, which may cause trouble. Perhaps Thomas (or
> Ross?)
> > > will see this and be able to comment. However I can't imagine it is
> > > necessary to use the softcore code since the proton likely has no
> > > Lennard-Jones term anyway. Even if that is not the case, I would guess
> > that
> > > the epsilon parameters are probably small enough that they can be
> scaled
> > > away linearly, although this is pure speculation.
> > >
> > > I would try using the normal TI code and setting lambda = 1 or 0 and
> > > verifying that you obtain the same dynamics you did with the QM/MM code
> > on
> > > its own.
> > >
> > > Regards,
> > > Brian
> > >
> > > On Mon, Feb 4, 2013 at 1:31 PM, Fabrício Bracht <bracht.iq.ufrj.br>
> > wrote:
> > >
> > > > What I meant is that I have already performed a MM ti simulation, but
> > > since
> > > > I am using soft core potentials, I cannot set Lambda = 1 or lambda =
> 0.
> > > > This means that I have not done such simulations (lambda = 0 or 1)
> with
> > > > qmmm either. Setting restraints to the bonds between the zinc atom
> and
> > > the
> > > > hydroxyl group has not worked either. The addition of these
> restraints
> > > > result in very abnormal behaviour, such as very distorted geometry of
> > the
> > > > entire qm region, as well as SCF failing to converge. What I still
> > don't
> > > > understand is why such abnormal behaviour happens only with TI
> > > simulations.
> > > > As I said before, if I simulate only the hydroxyl system (no
> > multisander
> > > > simulation with the HOH system) with qmmm, the simulation runs
> > smoothly.
> > > Do
> > > > you imagine I will have more success doing Ti simulation without
> > softcore
> > > > potentials?
> > > > Fabrício Bracht
> > > >
> > > > 2013/2/3 Brian Radak <radak004.umn.edu>
> > > >
> > > > > Fabricio,
> > > > >
> > > > > So do you mean that setting lambda = 1.0 or 0.0 with the TI code
> > gives
> > > > > different results than the QM/MM code on its own? That would be
> > > > concerning
> > > > > indeed. I'm pretty sure that, all else equal, running an NVE
> > simulation
> > > > > (ntt = 0) or setting ig to an explicit value should result in
> > identical
> > > > > trajectories for both of those circumstances, even with multiple
> > > > > processors. That is the most simplest and most obvious test that I
> > can
> > > > > think of (nstlim = 10, ntpr = 1, etc. should be adequate).
> > > > >
> > > > > As for the alternate transformation method, I am not sure how much
> > this
> > > > is
> > > > > done in the literature, but the idea would be to have the proton
> > > > > "disappear" via an MM transformation with an appropriate force
> field
> > > (in
> > > > > principle this can be arbitrary). Then, one would perform two
> > > additional
> > > > > transformations from the MM endpoints where one endpoint is the MM
> > > > > description and the other is the analogous QM/MM description. This
> > > should
> > > > > in principle amount to a smaller perturbation of the bonded and
> > > > > electrostatic terms (no guarantees!) as well as avoid the "problem"
> > of
> > > > > having weird bonded terms on the QM atoms.
> > > > >
> > > > > I have no idea if the latter suggestion would solve your
> instability
> > > > > issues, but if no other solutions present themselves it's probably
> > > worth
> > > > a
> > > > > try.
> > > > >
> > > > > Regards,
> > > > > Brian
> > > > >
> > > > > On Sat, Feb 2, 2013 at 8:33 PM, Fabrício Bracht <bracht.iq.ufrj.br
> >
> > > > wrote:
> > > > >
> > > > > > Hi Brian. Thank you for the advice. Indeed I had already seen the
> > > > > article,
> > > > > > but I think it is time to read it again with more attention. The
> > > lambda
> > > > > > values I am using are 0.01592; 0.08198; 0.19331; 0.33787; 0.5;
> > > 0.66213;
> > > > > > 0.80669; 0.91802; 0.98408. These are the values listed in amber12
> > > > manual
> > > > > > page #117.
> > > > > > The odd thing though is the difference I get in behaviour when I
> > run
> > > > the
> > > > > > simulation still with qmmm and using the same basic input
> > parameters;
> > > > > i.e.,
> > > > > > using the same input file as for the TI calculation, but without
> > the
> > > TI
> > > > > > part. All atoms stay bound, no matter what happens. At least for
> > the
> > > > > > hydroxyl ligand. I was, indeed, expecting some problems to arise
> > with
> > > > the
> > > > > > water molecule, since an oxygen atom bound to two hydrogens and a
> > > zinc
> > > > > atom
> > > > > > is unlikely to stay that way for long.
> > > > > > You mentioned doing a MM simulation. Well, I already did that,
> > but I
> > > > am
> > > > > > not sure I understood what you meant by "perform MM to QM/MM
> > > > > > transformations on the endpoints as a kind of correction."
> > > > > > Thank you again
> > > > > > Fabrício Bracht
> > > > > >
> > > > > >
> > > > > > 2013/2/2 Brian Radak <radak004.umn.edu>
> > > > > >
> > > > > > > Hi Fabricio,
> > > > > > >
> > > > > > > Can you clarify what exactly you mean by "start with the TI
> > > > > simulation"?
> > > > > > > What values of lambda? Does this behavior occur for all of
> them?
> > > > > > >
> > > > > > > Some other things that might be informative: What
> topolog(y/ies)
> > > are
> > > > > you
> > > > > > > using? What bonded terms exist on the protons?
> > > > > > >
> > > > > > > I believe the best established QM/MM protocols for pKa type
> > > > > calculations
> > > > > > > involve some kind of restraints, but how you choose to apply
> them
> > > is
> > > > > > still
> > > > > > > something of an art. The following paper describes a protocol
> in
> > > > > CHARMM,
> > > > > > > but I'm pretty sure the ideas transfer well to AMBER:
> > > > > > >
> > > > > > > Li and Qiang, J Phys Chem B 2003, 107, 14521.
> > > > > > >
> > > > > > > I attempted similar calculations a while back but had a very
> > > > difficult
> > > > > > time
> > > > > > > getting reproducible results. I suspect that there are some
> zero
> > of
> > > > > > energy
> > > > > > > issues that need to be handled when you have the same number of
> > > > > electrons
> > > > > > > but different orbitals. I am not sure what the solution is
> there.
> > > An
> > > > > > > alternative path is to perform the proton disappearing as an MM
> > to
> > > MM
> > > > > > > mutation and then perform MM to QM/MM transformations on the
> > > > endpoints
> > > > > > as a
> > > > > > > kind of correction. This is more work but I suspect will
> converge
> > > > > faster
> > > > > > in
> > > > > > > most situations.
> > > > > > >
> > > > > > > Regards,
> > > > > > > Brian
> > > > > > >
> > > > > > > On Sat, Feb 2, 2013 at 2:35 PM, Fabrício Bracht <
> > bracht.iq.ufrj.br
> > > >
> > > > > > wrote:
> > > > > > >
> > > > > > > > Hi all. I am doing a TI caltulation in order to obtain the
> free
> > > > > energy
> > > > > > > > values associated with the loss of a proton from a hydroxyl
> > group
> > > > > bound
> > > > > > > to
> > > > > > > > a zinc atom coordinated with 3 other aminoacids. System 1
> > > comprises
> > > > > of
> > > > > > a
> > > > > > > > water molecule bound to the zinc atom, and system 2 is the
> > > hydroxyl
> > > > > > > group.
> > > > > > > > When I run qmmm simulations, using DFTB, of both systems
> > > > separately,
> > > > > > the
> > > > > > > > system stays intact, i.e. no bonds are broken and both the
> > water
> > > > and
> > > > > > the
> > > > > > > > hydroxyl stay bound to the zinc atom ( as was expected). But
> as
> > > > soon
> > > > > > as I
> > > > > > > > star with the TI simulation, the hydroxyl group always drifts
> > > away.
> > > > > > > > Sometimes the oxygen atom stays and the hydrogen goes for a
> > walk.
> > > > > This
> > > > > > > > happens only on TI simulations and the water system stays
> > > intact. I
> > > > > > have
> > > > > > > > tried different sizes of qm region, different cutoffs, tried
> > > > several
> > > > > > > > different starting structures ( minimized, equilibrated,
> > > > thermalized
> > > > > > etc)
> > > > > > > > and the result is almost always the same. Below is the input
> > file
> > > > for
> > > > > > the
> > > > > > > > hydroxyl group system. I thought about restraining the
> hydroxyl
> > > > group
> > > > > > > using
> > > > > > > > the nmropt module. Can I use the dvdl_norest flag to ignore
> > those
> > > > > > > > restraints in the energy calculation? Please let me know if
> you
> > > > need
> > > > > > any
> > > > > > > > other detail from the simulation and/or if you need/want any
> > file
> > > > > from
> > > > > > > the
> > > > > > > > inputs.
> > > > > > > > Thank you
> > > > > > > > Fabrício Bracht
> > > > > > > >
> > > > > > > > TI of hydroxyl group step 1
> > > > > > > > &cntrl
> > > > > > > > imin = 0,
> > > > > > > > irest = 1,
> > > > > > > > ntx = 7,
> > > > > > > > ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
> > > > > > > > cut = 8.0,
> > > > > > > > ntr = 0,
> > > > > > > > ntc = 2,
> > > > > > > > ntf = 1,
> > > > > > > > temp0 = 298.0,
> > > > > > > > ntt = 3,
> > > > > > > > gamma_ln = 1.0,
> > > > > > > > nstlim = 1000000, dt = 0.0005, ntave = 100,
> > > > > > > > ntpr = 100, ntwx = 100, ntwr = 100,
> > > > > > > > ig = 10703, ioutfm = 1, iwrap = 1,
> > > > > > > > icfe = 1, ifsc = 1, clambda = 0.01592,
> > > > > > > > ifqnt = 1, scmask = ':342', idecomp = 0, nmropt = 0,
> > > > > > > > /
> > > > > > > > &qmmm
> > > > > > > > qmmask=
> > > > > > > >
> > > > ':200,255,258&!.CA,C,HA,O,N,HN,H|:341,342|(:202,204&!.CA,C,HA,O,N,H)'
> > > > > > > > dftb_3rd_order = 'PA'
> > > > > > > > qmcharge=-1,
> > > > > > > > qm_theory='DFTB',
> > > > > > > > qmshake=0,
> > > > > > > > qm_ewald=1, qm_pme=1
> > > > > > > > qmcut=9.0
> > > > > > > > writepdb=1
> > > > > > > > /
> > > > > > > > Receptor residues
> > > > > > > > RRES 1 7853
> > > > > > > > END
> > > > > > > > Printing
> > > > > > > > RES 1 342
> > > > > > > > END
> > > > > > > > END
> > > > > > > > _______________________________________________
> > > > > > > > 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
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> > > > > > >
> > > > > > _______________________________________________
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> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > ================================ 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.
> > > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
> > > ================================ 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.
> > > _______________________________________________
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> > >
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> > 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.
> _______________________________________________
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Received on Mon Feb 04 2013 - 12:30:02 PST
