From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Dec 10 2012 - 12:20:07 CST
Rajan,
May I ask how you did the start and restart exactly? Did you build a new
pdb file in vmd and start with that after the Langevin dynamics were done?
Thanks,
Eddie
On Mon, Dec 10, 2012 at 11:00 AM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> 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
> >
> >
>
>
-- Eddie
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:21 CST