Hi,
First, after thinking about this a bit more, I don't think my method would
work very well for the same reason that you need to unwrap your trajectory
prior to calculating diffusion from MSD, namely your water molecules will
have "jumps" that will artificially increase their MSD for a frame. You
would need to detect and discount such jumps; this is probably a good
feature to add.
On Sat, Jul 12, 2014 at 10:01 AM, newamber list <newamberlist.gmail.com>
wrote:
>
> Also manual suggests to use unwrap before performing diffusion analysis.
> Please correct me, this would mean the particles (ions/waters) 'fly away'
> from the solute (relatively faster than solute itself) compared to the
> starting packed box and I should see randomly distributed particles all
> around the solute. Considering this unwrap tarjectory, then a very long
> simulation would make solute dried out of water.
>
Remember that when you are simulating with PBC, your water doesn't "fly
away" from the solvent, it merely enters a neighboring unit cell and
interacts with the solute "image". So you will never (and can never) have a
dry solute with PBC (but of course if you turn off PBC then you will
eventually dry out).
> Actually my volume of interest is near the center of solute itself so I
> will get less waters to average my results. Unwrap will make all particles
> diffused far away from center of solute. In this case would you suggest me
> to use imaged trajectory?
>
This really won't work with the diffusion command as currently written for
the reason I stated above. You'll have to calculate this manually for now.
You can maybe do this with the output from diffusion and a script. You'll
want to leave out the 'average' keyword so you have the raw MSD output for
each molecule; then you can detect when a jump occurs and discount it.
Good luck,
-Dan
>
> Thanks for any suggestions.
>
>
>
>
>
> On Fri, Jul 11, 2014 at 9:41 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > Hi Daniel
> >
> > Thanks for your help and suggestions that you always render. So saying
> > this I think following approach should work:
> >
> > Actually I have some volume selection criteria that my script can handle
> > and tell which waters are there in that volume in each frame, thus having
> > this info I should do this:
> >
> > Lets say at time t1 I know one water molecule in some volume I am
> > interested in. Then I should find time t2 such that this water molecule
> > stays continuously in that volume. This will give small chunk (t2 - t1),
> > may be only few ps, of trajectory during which that water stays
> > continuously. Now I can calculate diffusion using cpptraj using specific
> > mask on that water. Yes also I will consider if that water molecule falls
> > back in that volume.
> >
> > Similarly this will be done for other waters starting at time t1 and thus
> > finally I will average and if standard deviation is very large then I
> > should consider changing volume size criteria.
> >
> >
> > regards,
> > JIom
> >
> >
> >
> > On Fri, Jul 11, 2014 at 8:57 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> On Fri, Jul 11, 2014 at 1:11 PM, newamber list <newamberlist.gmail.com>
> >> wrote:
> >>
> >> > I have some general query regarding diffusion. cpptraj diffusion
> command
> >> > says
> >> > 'In order to correctly calculate diffusion molecules should take
> >> > continuous paths'
> >> >
> >>
> >> This just means that you should not have any imaging artifacts in your
> >> trajectory (i.e. when your molecule "wraps" from one side of your cell
> to
> >> the opposite side), otherwise you will artificially inflate the
> "velocity"
> >> of that molecule for that frame.
> >>
> >>
> >> >
> >> > Ideally how long this path should be? infinite or some finite (if
> >> finite,
> >> > then how much?). I am asking because somehow I am interested to know
> >> local
> >> > diffusion in very small volume and as its a very small volume so one
> can
> >> > not expect the same molecule to stay longer inside that volume and
> >> > molecules will be exchanging quickly with molecules outside the
> >> considered
> >> > box. Thus smaller will be the continuous path it will travel if moves
> >> out
> >> > volume quickly.
> >> >
> >>
> >> If I understand what you are proposing to do, then it is currently very
> >> difficult to do with cpptraj. You can calculate diffusion from the
> >> mean-square displacement (MSD) using the Einstein relation:
> >>
> >> 2*n*D = lim(t->inf) MSD / t
> >>
> >> The key is that this relation is valid as t approaches infinity,
> otherwise
> >> your data will be too noisy; this is why the manual recommends averaging
> >> over many atoms (in other words calculate diffusion for all waters, not
> >> just one). What you would need to do is somehow filter out all waters
> >> except those in the area of interest. You could *maybe* do this if the
> >> area
> >> of interest is near some solute which can be used as a reference point,
> >> then you use the "closest" command to retain a certain number of waters
> >> near that area of solute. You would need to make sure you have enough
> >> atoms
> >> and enough frames so that you are getting a good estimate of the
> diffusion
> >> constant though; you would probably want to do something like see how
> your
> >> answer changes vs the number of waters you add in etc.
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >>
> >>
> >> >
> >> > Any suggestions will be really helpful
> >> >
> >> > Thanks
> >> > JIom
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jul 12 2014 - 11:30:02 PDT
