**From:** Josep Ivan Balaguer Molins (*jobamo1_at_etsid.upv.es*)

**Date:** Tue Jul 31 2018 - 01:24:58 CDT

**Next message:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Previous message:**Jérôme Hénin: "Re: 1-D ABF and Compressibility"**In reply to:**Brian Radak: "Re: Problems with temperature control."**Next in thread:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Reply:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thank you very much Brian. I've turned off the pressure control. And

I've changed the temperature increment from -10 to -0.1 and even to

-0.001:

run 1000

for { set TEMP 600 } { $TEMP >= 300 } { incr TEMP -0.1 } {

reassignTemp $TEMP

run 1000

}

reassignFreq 100

In any case I get the warning "low global exclusion count" as you

expected before. And the simulation stops:

ERROR: Constraint failure in RATTLE algorithm for atom 1347!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 9897!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 12147!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 8997!

ERROR: Constraint failure; simulation has become unstable.

I've read this:

http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting

I've increased the margin from 4 to even 20 without succes. The same

atoms become unestable. I've decreased the reassingFreq but it doesn't

solve the problem either.

Any idea?

Thank you very much.

Ivan

Quoting Brian Radak <brian.radak_at_gmail.com>:

*> Sorry, I meant reassignFreq. In any event, that is not what is apparently
*

*> causing the error.
*

*>
*

*> I'm actually not sure why you would get a low global bond count (I might
*

*> have expected a low global exclusion count). My guess is the system is
*

*> cooling too quickly and thus pressure control is causing issues. In
*

*> retrospect, the pressure control is probably not a good idea in this case,
*

*> since your temperature change is very large.
*

*>
*

*> On Mon, Jul 30, 2018 at 10:41 AM, Josep Ivan Balaguer Molins <
*

*> jobamo1_at_etsid.upv.es> wrote:
*

*>
*

*>> Sorry, Brian but I don't understand... Here is the code were I get the
*

*>> error.
*

*>>
*

*>>
*

*>> #############################################################
*

*>> ## ADJUSTABLE PARAMETERS ##
*

*>> #############################################################
*

*>> gromacs on
*

*>> grotopfile 32x50LA_crystal.top
*

*>> grocoorfile 32x50LA_crystal.gro
*

*>> bincoordinates testD2.coor
*

*>>
*

*>> paraTypeCharmm on
*

*>> exclude scaled1-4
*

*>> 1-4scaling 0.5
*

*>>
*

*>> switching on
*

*>> switchdist 8 # at 8Å we start to smooth electrostatic to 0
*

*>> cutoff 12.0
*

*>> pairlistdist 26.0
*

*>> margin 4
*

*>>
*

*>> # Integrator Parameters
*

*>>
*

*>>
*

*>>
*

*>> rigidBonds all ;# needed for 2fs steps
*

*>> nonbondedFreq 1
*

*>> vdwGeometricSigma yes
*

*>> fullElectFrequency 2
*

*>> stepspercycle 20
*

*>> pairlistsperCycle 2
*

*>>
*

*>> wrapAll on
*

*>>
*

*>> timestep 1.0 ;# 2fs/step 2 en simulación, 1 minimizacion
*

*>>
*

*>> outputEnergies 100
*

*>> outputtiming 100
*

*>> outputPressure 100
*

*>> binaryoutput yes
*

*>> outputname testD3
*

*>> dcdfreq 200
*

*>> restartfreq 1000
*

*>> restartname rest_TestD3
*

*>>
*

*>> binvelocities testD2.vel
*

*>>
*

*>> reassignFreq 100
*

*>> run 80
*

*>> for { set TEMP 550 } { $TEMP >= 300 } { incr TEMP -10 } {
*

*>> reassignTemp $TEMP
*

*>> run 100
*

*>> }
*

*>>
*

*>>
*

*>>
*

*>>
*

*>> # Constant Temperature Control
*

*>>
*

*>> langevin off ;# do langevin dynamics
*

*>> langevinDamping 2 ;# damping coefficient (gamma) of 1/ps
*

*>> langevinTemp 300
*

*>> langevinHydrogen no ;# don't couple langevin bath to hydrogens
*

*>> langevinPiston on
*

*>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
*

*>> langevinPistonPeriod 10000
*

*>> langevinPistonDecay 15000
*

*>> langevinPistonTemp 300
*

*>>
*

*>> useGroupPressure yes ;# needed for rigidBonds
*

*>> useFlexibleCell no
*

*>> useConstantArea no
*

*>>
*

*>> extendedSystem testD2.xsc
*

*>>
*

*>> run 300000
*

*>>
*

*>>
*

*>> I don't have a reassignIncr here... or do you mean I have to make it
*

*>> smaller on the previous minimization and simulation?
*

*>> If I turn langevin off, tha same error appears.
*

*>>
*

*>> Thank you very much for your answer.
*

*>>
*

*>> Best regards
*

*>>
*

*>> Ivan
*

*>>
*

*>>
*

*>> Quoting Brian Radak <brian.radak_at_gmail.com>:
*

*>>
*

*>> Note that the Langevin and reassign thermostats are completely decoupled
*

*>>> code paths. My guess is that the reassignIncr is too large compared to the
*

*>>> relaxation rate dictated by Langevin damping and the two are redundant -
*

*>>> personally I would only use one or the other (you can also script changes
*

*>>> to langevinTemp). You could also try using a smaller damping coefficient,
*

*>>> but this really isn't any different from not using Langevin at all.
*

*>>>
*

*>>>
*

*>>> On Mon, Jul 30, 2018 at 6:21 AM, Josep Ivan Balaguer Molins <
*

*>>> jobamo1_at_etsid.upv.es> wrote:
*

*>>>
*

*>>> Hi everyone!
*

*>>>>
*

*>>>> I have a system I've minimized and during minimization, it's been heat up
*

*>>>> to 600K using this code lines:
*

*>>>>
*

*>>>> temperature 0
*

*>>>>
*

*>>>> reassignFreq 1000
*

*>>>> reassignIncr 10
*

*>>>> reassignHold 600 # Final temperature
*

*>>>>
*

*>>>> langevin on ;# do langevin dynamics
*

*>>>> langevinDamping 2 ;# damping coefficient (gamma) of 1/ps
*

*>>>> langevinTemp 600 # Final temperature
*

*>>>> langevinHydrogen no ;# don't couple langevin bath to hydrogens
*

*>>>>
*

*>>>> langevinPiston on
*

*>>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
*

*>>>> langevinPistonPeriod 200
*

*>>>> langevinPistonDecay 100
*

*>>>> langevinPistonTemp 600 # Final temperature
*

*>>>>
*

*>>>> It does work, I can see the temperature converging to 600K in VMD.
*

*>>>>
*

*>>>> After this, I perform an Isothermal simulation to see if the systems
*

*>>>> keeps
*

*>>>> the stability and works too:
*

*>>>>
*

*>>>> binvelocities testD1.vel # Use velocities from minimization output.
*

*>>>>
*

*>>>> langevin on ;# do langevin dynamics
*

*>>>> langevinDamping 2 ;# damping coefficient (gamma) of 1/ps
*

*>>>>
*

*>>>> langevinTemp 600 # I keep the 600K
*

*>>>>
*

*>>>> langevinHydrogen no ;# don't couple langevin bath to hydrogens
*

*>>>>
*

*>>>> useGroupPressure yes ;# needed for rigidBonds
*

*>>>> useFlexibleCell no
*

*>>>> useConstantArea no
*

*>>>>
*

*>>>> langevinPiston on
*

*>>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
*

*>>>> langevinPistonPeriod 200
*

*>>>> langevinPistonDecay 100
*

*>>>> langevinPistonTemp 600 # I keep the 600K
*

*>>>>
*

*>>>> extendedSystem testD1.xsc
*

*>>>>
*

*>>>> run 400000
*

*>>>>
*

*>>>> Seeing the result in VMD, the code works well and the simulation has no
*

*>>>> errors, the temperature is stable at 600K.
*

*>>>>
*

*>>>> Finally to perform the final simulation, I have to cool the system down
*

*>>>> to
*

*>>>> 300K. So I use the output files and with Langevin I am able to cool down
*

*>>>> the sistem without problems to 300K. But seeing in VMD the temperature
*

*>>>> graph, the temperature goes down so fast. In 5000 integration steps goes
*

*>>>> from 600K to 300K. So I need to change the temperature graph. To do so, I
*

*>>>> use this code:
*

*>>>>
*

*>>>> binvelocities testD2.vel
*

*>>>>
*

*>>>> reassignFreq 100
*

*>>>>
*

*>>>> run 1000
*

*>>>>
*

*>>>> for { set TEMP 550 } { $TEMP >= 300 } { incr TEMP -10 } {
*

*>>>> reassignTemp $TEMP
*

*>>>>
*

*>>>> run 100
*

*>>>> }
*

*>>>>
*

*>>>> And I get the following error: FATAL ERROR: Bad global bond count! (14395
*

*>>>> vs 14400)
*

*>>>>
*

*>>>> How is that possible taking into account that before everything worked?
*

*>>>>
*

*>>>> Changing cutoff and pairlistdist parameters, I got it down to 14397
*

*>>>> instead of 14395. But I can get any better. And I don't understand why is
*

*>>>> this happening.
*

*>>>>
*

*>>>> Thank you very much.
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>>>
*

*>>
*

*>>
*

**Next message:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Previous message:**Jérôme Hénin: "Re: 1-D ABF and Compressibility"**In reply to:**Brian Radak: "Re: Problems with temperature control."**Next in thread:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Reply:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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