Re: Constraint failure; simulation has become unstable

From: Athanassios Stavrakoudis (astavrak_at_cc.uoi.gr)
Date: Sat Jan 08 2011 - 08:05:15 CST

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 González 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

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