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
> > > > >
> ====================================================================
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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
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> > appropriate
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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
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> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Mon Feb 04 2013 - 11:30:03 PST
