From: Josep Ivan Balaguer Molins (jobamo1_at_etsid.upv.es)
Date: Mon Jul 30 2018 - 05:21:09 CDT
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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