Hi Daniel,
Sorry, with drying out I meant if I save a pdb (which is non-PBC) I will
see my particles diffused away from solute. Actually my script reads pdb
only, so I think I should rmsd fit my solute and image my trajectory (and
write pdb) to select ions inside volume of my interest and do diffusion
analysis on those ions with unwrapped trajectory.
>> You would need to detect and discount such jumps;
If am not wrong, do you actually meant same thing that I should find small
chunk of trajectory when my particle is in that volume of interest as I
explained before?
best regards
On Sat, Jul 12, 2014 at 7:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
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> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> 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
> > >>
> > >
> > >
> > _______________________________________________
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> > 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
>
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Received on Sat Jul 12 2014 - 14:00:02 PDT
