Re: minimization, slow heating and then Langevin free runs

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Mon Dec 10 2012 - 11:00:40 CST

Hi Eddie,
        Unfortunately, as Norman Geist suggested, the best way to accomplish
what I was trying to do was to set up multiple conf files. I looked into
the "checkpoint" keyword as well, but I couldn't find enough details to
figure out how to use it properly. It sounds like you're encountering a
similar situation.
        My obsessive-compulsive side really wanted to keep my directories
simple by using only one conf file and one set of output files, but
separating things was just easier. If you find out how to use the
checkpoint/revert keywords, I'm sure there are a lot of people out there
that could use a few pointers.

Good luck,

Rajan

On Mon, 2012-12-10 at 09:08 -0600, Dr. Eddie wrote:
> 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, 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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