From: Wendy González (locuswendy_at_gmail.com)
Date: Sat Jan 08 2011 - 08:29:37 CST
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.
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 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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