Re: Constraint failure; simulation has become unstable

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 10 2011 - 08:49:07 CST

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2011/1/8 Wendy González <locuswendy_at_gmail.com>:
> But the idea is that if you are comparing three systems (see my first
> email), and A and C run properly, I can not do changes in parameters only in
> simulation B because it did not work. If I changes the parameters for B
> until it runs in 2.7 version, I have to do the same changes later in A and
> C.
> Solution:
> B run in 2.6 version
> A run already in 2.6 version
> I will run C in 2.6 version too.
> All the systems with the same parameters to do comparisons later.

wendy,

you are making a big mistake.
the fact, that one your simulations runs through with
NAMD 2.6 but fails with NAMD 2.7 doesn't necessarily
mean, that the v2.6 simulation is correct and the 2.7
ones are not. you have to have more compelling
evidence to convince people. sometimes you may
have a borderline failing case that completes or fails
with a slightly modified source or due to different
order of summation. that is usually an indication of
a bad model, not a bad code.

you have to provide corroborating evidence.

in general, your simulation strategy, and particularly
the use of "reload charges" seems very strange to me.
reassigning changes can add a significant (and unphysical)
"kick" to the system and perfectly explain your observations,
if the changes to the charges are misdirected or too large.
have you looked at the total energy overall, also in the
v2.6 case? have you looked at a high resolution trajectory
of the atoms giving the constraint failures?
overall, what is the rationale, behind using this feature
and what do you expect to learn from this?
i think particularly the last question is something that should
be discussed _first_ before worrying about whether the
simulation completes or not.

cheers,
axel.

>
> Regards,
>
> Wendy
>
> 2011/1/8 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>
>>
>> Wendy,
>>
>> Though I am not fully qualified to speak about the version differences,
>> I can say that NAMD is a very strong program in MD simulations.
>> Moreover I think that most of the "some thousands" publications made with
>> NAMD
>> came from version betas...
>> Some problems might rise, perhaps due to system setup.
>> But you have to deal with these.
>> The game is not like "push the button Max".
>>
>> All the best,
>> Thanassis
>>
>> > Dear NAMD Users:
>> >
>> > Thanks a lot for your comments. I found already the problem:
>> >
>> > It is NAMD2.7, I run my simulation with NAMD 2.6 and it worked.
>> >
>> > I am very disappointed with NAMD because this situation have been
>> > occurred
>> > several times with other simulations where I can not find a real
>> > solution to
>> > the problem. Then, I run the same simulation in NAMD2.6 without changes
>> > in
>> > any variable and it works properly. It was happening to me with
>> > NAMD2.7b2
>> > and NAMD2.7b3 versions, and I justified the fact due to they were still
>> > Beta versions, but it happened again, and now with 2.7 official version!
>> >
>> > :-(
>> >
>> > Regards,
>> >
>> > Wendy
>> >
>> >
>> >
>> > 2011/1/7 Joshua Adelman <jla65_at_pitt.edu>
>> >
>> > > Hi Wendy,
>> > >
>> > > When you're playing around with your charges in all of your systems
>> > > (and
>> > > with the reloadCharges command), are you making sure that your total
>> > > system
>> > > is neutral? I'm not that familiar with the reloadCharges command, but
>> > > it
>> > > seems like something you should only be messing around with for
>> > > special
>> > > purposes and not for general simulations.
>> > >
>> > > Also, if you're patching residues in your system, are you making sure
>> > > that
>> > > you've regenerated the angles and dihedrals correctly? If you are
>> > > using the
>> > > autopsfgen gui to build the system, then you need to select the option
>> > > in
>> > > the pull down menu. You can probably tell from inspection if your
>> > > patched
>> > > hydrogens are making strange angles/folding back on the residue. I
>> > > forgot
>> > to
>> > > do this once and I saw similar problems to what you are experiencing,
>> > > even
>> > > for small time steps. You might want to increase the output frequency
>> > > of
>> > the
>> > > dcd and see if you can spot what is going on immediately before things
>> > > crash.
>> > >
>> > > Best wishes,
>> > > Josh
>> > >
>> > >
>> > >
>> > > On Jan 7, 2011, at 4:18 PM, Wendy Gonzαlez wrote:
>> > >
>> > > Dear Athanassios:
>> > >
>> > > The fact is that I use the same script (see below) in the 3 systems
>> > > (they
>> > > change only in the charge of one histidine residue), and only one of
>> > > them
>> > > have problems, the other run normally.
>> > > This is my script:
>> > >
>> > > #############################################################
>> > > ## ADJUSTABLE PARAMETERS ##
>> > > #############################################################
>> > >
>> > > structure ionized.psf
>> > > coordinates DM_5ns_only_70.coor
>> > > velocities DM_5ns_only_70.vel
>> > > extendedSystem DM_5ns_only_70.xsc
>> > > parameters par_all27_lipid.prm
>> > > parameters par_all22_prot_cmap.inp
>> > > paraTypeCharmm on
>> > >
>> > >
>> > > #############################################################
>> > > ## SIMULATION PARAMETERS ##
>> > > #############################################################
>> > >
>> > >
>> > > # Force-Field Parameters
>> > > exclude scaled1-4
>> > > 1-4scaling 1.0
>> > > cutoff 12.0
>> > > switching on
>> > > switchdist 10.0
>> > > pairlistdist 13.5
>> > >
>> > > # Integrator Parameters
>> > > timestep 0.5 ;# 1fs/step (2)
>> > > rigidBonds all ;# needed for 1fs steps (2)
>> > > nonbondedFreq 2
>> > > fullElectFrequency 4
>> > > stepspercycle 20
>> > >
>> > > # Constant Temperature Control
>> > > langevin on ;# do langevin dynamics
>> > > langevinDamping 1.0 ;# damping coefficient (gamma) of 10/ps (5)
>> > > langevinTemp 300
>> > > langevinHydrogen no ;# don't couple langevin bath to hydrogens
>> > >
>> > > # use lighter damping now that system is equilibrated
>> > > langevinPiston on
>> > > langevinPistonTarget 1.01325
>> > > langevinPistonPeriod 200
>> > > langevinPistonDecay 500
>> > > langevinPistonTemp 310
>> > >
>> > > useGroupPressure yes # smaller fluctuations
>> > > useFlexibleCell yes # allow dimensions to fluctuate
>> > > independently
>> > > useConstantRatio yes # fix shape in x-y plane
>> > >
>> > > margin 2
>> > >
>> > > wrapAll on
>> > >
>> > > # PME (for full-system periodic electrostatics)
>> > > PME yes
>> > > PMEGridSizeX 103
>> > > PMEGridSizeY 103
>> > > PMEGridSizeZ 88
>> > >
>> > >
>> > > # Output
>> > > binaryoutput no
>> > > outputEnergies 10000
>> > > outputTiming 10000
>> > > xstFreq 10000
>> > > dcdFreq 10000
>> > > restartfreq 10000
>> > >
>> > > ############################################
>> > >
>> > > if {1} {
>> > > constraints on
>> > > consRef restrain_ca_not_filter.pdb
>> > > consKFile restrain_ca_not_filter.pdb
>> > > consKCol B
>> > > }
>> > >
>> > > ##############################################################
>> > > outputname DM_5ns_E70x6times
>> > > run 10000
>> > > reloadCharges charges_only_task3_E70x6times.txt
>> > > run 5000000
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > 2011/1/7 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>
>> > >
>> > >>
>> > >> Dear Wendy,
>> > >>
>> > >> Multiple reasons may lead to this situation.
>> > >> Most possibly, your system is not well minimized/equilibrated.
>> > >> You need to give a more detailed description of your simulation
>> > >> setup, to get more detailed answer.
>> > >> Also search the NAMD-l archives, almost any user has come with this
>> > >> problem.
>> > >>
>> > >> You can try to decrease the timestep to 1 fs,
>> > >> or to decrease the nonbondedFreq, fullElectFrequency values.
>> > >> Or to experiment with a mixture of all of these.
>> > >>
>> > >> Good luck,
>> > >> Thanassis
>> > >> > Dear NAMD Users,
>> > >> >
>> > >> > I am working with 3 systems, the only difference between them are:
>> > >> >
>> > >> > a) 2 histidines protonated
>> > >> > b) 1 histidine protonated, the second is neutral
>> > >> > c) Both histidines neutral
>> > >> >
>> > >> > I run several nanoseconds of simulations on this systems and they
>> > >> > did
>> > >> not
>> > >> > have problems. I applied the reloadCharges command (increasing the
>> > >> charge of
>> > >> > the same glutamate in the 3 systems) and the results are:
>> > >> >
>> > >> > a) Run normally
>> > >> > b) ERROR: Constraint failure in RATTLE algorithm for atom XXXX
>> > >> > ERROR:
>> > >> > Constraint failure; simulation has become unstable.
>> > >> > c) Run normally
>> > >> >
>> > >> > In case b) I said "atom XXXX", because I run 3 different
>> > >> > simulations and
>> > >> the
>> > >> > error is with a different atom each time.
>> > >> >
>> > >> > Any suggestion??? What could be happening???
>> > >> >
>> > >>
>> > >>
>> > >>
>> > >> Athanassios Stavrakoudis
>> > >> University of Ioannina web:
>> > >> http://stavrakoudis.econ.uoi.gr/
>> > >> Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
>> > >> GR-45110, Ioannina tel: +30 265 100 5935
>> > >> GREECE fax: +30 265 100 5092
>> > >>
>> > >
>> > >
>> > >
>> > >
>> >
>>
>>
>>
>> Athanassios Stavrakoudis
>> University of Ioannina web:
>> http://stavrakoudis.econ.uoi.gr/
>> Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
>> GR-45110, Ioannina tel: +30 265 100 5935
>> GREECE fax: +30 265 100 5092
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

Next message: Seren Soner: "Error on closing binary file"
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In reply to: Wendy Gonz�lez: "Re: Constraint failure; simulation has become unstable"
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