From: Wendy González (locuswendy_at_gmail.com)
Date: Sat Jan 08 2011 - 07:53:11 CST
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
>>
>
>
>
>
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