Re: minimization, slow heating and then Langevin free runs

From: Dr. Eddie (eackad_at_gmail.com)
Date: Mon Dec 10 2012 - 15:00:56 CST

Yes, if you don't mind that would be great. I have some idea of how to do
what you describe but seeing it would really help!

On Mon, Dec 10, 2012 at 1:33 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:

> Eddie,
> I usually start with a PDB/PSF that comes from VMD, and using the
> default setting:
>
> binaryoutput yes
>
> I receive a .coor, .vel, and a .xsc file from the first (NpT)
> simulation. This simulation minimizes and equilibrates the system at a
> variable volume.
> The next simulation, NVT, receives the following input from the NpT
> simluation:
>
> binCoordinates NpT.coor
> binVelocities NpT.vel
>
> I find the average volume that was produced from the NpT simulation
> after the volume stops changing drastically, and this number is set as
> the fixed volume with the lines:
>
> cellBasisVector1 xvector 0 0
> cellBasisVector2 0 yvector 0
> cellBasisVector3 0 0 zvector
> cellOrigin 0 0 0
>
> where xvector*yvector*zvector is your total volume. NVT runs and outputs
> the same as the NpT simulation, and this time I use all three
> (.vel, .coor, and .xsc) files as inputs to the NVE simulation.
>
> binCoordinates NVT.coor
> binVelocities NVT.vel
> extendedSystem NVT.xsc
>
> Because in the NVE simulation I am using the .xsc file to
> determine the
> PBC boundaries, I comment out the cellBasisVector lines. Note that going
> from NpT to NVT sometimes produces erroneously high energies. Basically
> the source of this problem is that you are taking a volume of your
> simulation (the average over the NpT) that doesn't necessarily
> correspond to the .vel and .coor files (which are just the snapshots of
> the last point in the NpT). If the volume of your last point is much
> different than the average, some strange things can happen as a result
> of the compression/expansion of your system. The way to detect if your
> system has suffered from this is to watch the energies of your system
> from NpT to NVT to NVE. If the system energy has changed drastically
> from NpT to NVE, and that change isn't just a result of a small T
> difference from removing the thermostat, then you'll have to find the
> coordinates and velocities from the .dcd file of a configuration where
> the volume is closer to your average volume. This is a complicated
> process, and even more complicated to describe without
> figures/equations, but the solution is simple.
> I can also send over my conf files if you would like.
>
> rajan
>
>
>
> On Mon, 2012-12-10 at 12:20 -0600, Dr. Eddie wrote:
> > 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
> >
> >
>
>

-- 
Eddie

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