minimization, slow heating and then Langevin free runs

From: Dr. Eddie (eackad_at_gmail.com)
Date: Sun Dec 09 2012 - 10:16:21 CST

Hi all,
I've been trying to setup a single config file that would do the
minimization, then slow heating with pressure equilibration and then turn
off the Langevin dynamics once the structure/solvent has reached the
desired temperature/pressure.

I have tried many things and would like some advice to make this work (if
it is possible) and ensure I'm not making some gross error.
The relevant part of the config file is (my number of timesteps is small so
I can see the crashes quickly)

langevin on
langevinDamping 1.
langevinTemp 100 # <---- 1st problem is if this (and all the
temperatures below) is lower than 100
                                       #REINITIALIZING VELOCITIES AT STEP
16 TO 25 KELVIN.
                                       #TCL: Running for 48 steps
                                       #FATAL ERROR: Periodic cell has
become too small for original patch grid!
langevinHydrogen no
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 100
temperature 100
for { set MIN 0 } { $MIN < 3 } { incr MIN 1 } {
   minimize 16
   reinitvels 100
   run 48
}

# I need to start my heating at 100 k (set TEMP 100 below) otherwise I also
get the error:
#TCL: Setting parameter langevinPistonTemp to 25
#TCL: Setting parameter langevinTemp to 25
#REINITIALIZING VELOCITIES AT STEP 192 TO 25 KELVIN.
#TCL: Running for 48 steps
#FATAL ERROR: Periodic cell has become too small for original patch grid!
for { set TEMP 100} { $TEMP < 285 } { incr TEMP 25 } {
   langevinPistonTemp $TEMP
   langevinTemp $TEMP
   reinitvels $TEMP
   run 48
}
temperature 310 #<------- If I use 100 K for minimization etc
This command fails with:
                                    #TCL: Setting parameter temperature to
310
                                    #FATAL ERROR: Setting parameter
temperature from script failed!
                                    # DO I need it?

langevinPistonTemp 310
langevinTemp 310
reinitvels 310
run 50000

langevinPiston off #<---- doing all of the above (which seems
dubious) this fails with:
                                  #TCL: Setting parameter langevinPiston to
off
                                  #TCL: Setting parameter langevin to off
                                  #FATAL ERROR: Setting parameter langevin
from script failed!
langevin off
run 20000000

I'd like to end up with a minimized, slowly heated system at the right
temperature/pressure. Then I'd like to run that system without the Langevin
forces on to see how much for the protein's sidechains alone move (rmsd,
distances to other CA's etc) without any random forces increasing the
distance.

Thank you very much for any help!
Eddie 

-- 
Eddie

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