From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jul 30 2018 - 13:31:20 CDT
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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