Re: minimization, slow heating and then Langevin free runs

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Sun Dec 09 2012 - 17:02:10 CST

Eddie,
        I ran into a similar problem as your last error message a while back:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14609.html

It's not possible to change all of the conf file keywords/variables
after the first "run" command in the conf file. Here's the page to read:

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node10.html

I haven't seen your first error before so I can't comment on that.

Good luck,

rajan

On Sun, 2012-12-09 at 10:16 -0600, Dr. Eddie wrote:
> 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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