From: Josep Ivan Balaguer Molins (jobamo1_at_etsid.upv.es)
Date: Tue Jul 31 2018 - 01:24:58 CDT
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.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
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