From: Josep Ivan Balaguer Molins (jobamo1_at_etsid.upv.es)
Date: Mon Jul 30 2018 - 09:41:32 CDT
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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