From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Dec 10 2012 - 09:08:05 CST
Thanks Rajan. So how did you "solve" turning the langevin dynamics off?
Restart the simulation somehow? Were you able to restart the simulation in
1 config file?
I know there are commands 'checkpoint' and 'revert', from
here<http://www.ks.uiuc.edu/Research/namd/2.6/ug/node11.html>,
but the documentation on these is scarce at best! It sounds like I should
be able to make a checkpoint and then revert back changing some system
parameters, but I have no idea how!
Thanks!
Eddie
On Sun, Dec 9, 2012 at 5:02 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> 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
> >
>
>
-- Eddie
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