Re: SMD behavior

From: Adam Fraser (adam.n.fraser_at_gmail.com)
Date: Sat Dec 01 2007 - 12:03:40 CST

Well, I tried adjusting the timesteps between my simulations AND changing
the SMDFile to use the output coordinates of the previous simulation. This
still didn't work, I think because I changed both.

So... I changed the SMDFile only. So the second simulation uses these
settings...
structure 2HEX_solv_HEAVY-16.psf #Even simulations
SMD on
SMDFile output/AFM_sim_previous.coor
SMDk 6.6
SMDVel 0.000016 #(A/fs) 20A/1200000fs
SMDDir 1 0 0 #
timestep 1.0
firsttimestep 0
numsteps 1200000

At last, this resulted in the pulling speed I expected. However, the
molecule is pulled in the direction (1 1 0) instead of (1 0 0)... this is
observed so it may be that the actual vector is circumstantial.

Is it possible that this is being caused by the SMDFile being used?

The first simulation works perfectly fine and uses the settings described in
my original message.

Does anyone have any suggestions to explain what is happening here?

-ADam

On Nov 24, 2007 1:27 PM, Adam Fraser <adam.n.fraser_at_gmail.com> wrote:

> Thanks tons poker! I'll try this.
>
> -Adam
>
>
> On Nov 21, 2007 7:18 PM, <poker_at_physics.usyd.edu.au> wrote:
>
> > Did you check your timesteps? Read the userguide on SMD - the constraint
> > position is determined based on velocity times the current timestep.
> > -> You'll need to change the timestep every simulation and/or change the
> >
> > reference file when you pull.
> >
> > Quoting Adam Fraser <adam.n.fraser_at_gmail.com>:
> >
> > > I am trying to push and pull a molecule in successive simulations as
> > is
> > > done
> > > in Atomic Force Microscopy (AFM).
> > >
> > > I've done this before and never had a problem with it until now and I
> > > can't
> > > figure out what's wrong.
> > >
> > > *The conditions:*
> > >
> > > During each "push" simulation, I use settings:
> > > structure 2HEX_solv_HEAVY-13-16.psf
> > > ..
> > > SMD on
> > > SMDFile 2HEX_SMD_PUSH.pdb
> > > SMDk 6.6
> > > SMDVel 0.000016 #(A/fs) 20A/1200000fs
> > > SMDDir -1 0 0
> > >
> > > During each "pull" simulation, I use settings:
> > > structure 2HEX_solv_HEAVY-16.psf
> > > ..
> > > SMD on
> > > SMDFile 2HEX_SMD_PULL.pdb
> > > SMDk 6.6
> > > SMDVel 0.000016 #(A/fs) 20A/1200000fs
> > > SMDDir 1 0 0
> > >
> > > 2HEX_SMD_PUSH.pdb selects 2 atoms to push whereas 2HEX_SMD_PULL.pdb
> > only
> > > selects one atom to pull.
> > >
> > > 2HEX_solv_HEAVY-13-16.psf specifies that the two pushed atoms are VERY
> > > heavy
> > > 2HEX_solv_HEAVY- 16.psf specifies that only the single pulled atom is
> > > VERY
> > > heavy
> > > ..all other atoms have normal mass
> > >
> > > eg:
> > > Hexadecane molecule: /\/\/\/\/\/\/\/\
> > > PUSH: /\/\/\/\/\/\/*\/\* <-- F
> > > PULL: /\/\/\/\/\/\/\/\* --> F
> > > *asterisks mark the atoms being pushed/pulled
> > >
> > > *What is happening:*
> > > During the first push simulation ONLY, the molecule is moving in the
> > -x
> > > direction 20Angstroms nice and smoothly over a period of 1.2ns.
> > >
> > > ALL remaining simulations (pull,push,pull,push...) behave
> > unexpectedly.
> > > The
> > > molecule moves VERY quickly backward and springs back and forth over
> > > ~30A
> > > distance about every 60ps. During this oscillation, the center of the
> >
> > > spring appears to be drifting in the direction of the applied force.
> > >
> > > I repeatedly compared the first push simulation to the others and
> > found
> > > no
> > > differences whatsoever that could account for the difference in
> > behavior
> > > I'm
> > > seeing.
> > >
> > > Does anyone have any ideas or suggestions to help me out with this
> > > problem?
> > > I'd greatly appreciate any help.
> > >
> >
> >
> >
> >
> > ----------------------------------------------------------------
> > This message was sent using IMP, the Internet Messaging Program.
> >
>
>

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