Hi Daniel,
Thanks this indeed is useful but would be helpful for radial distribution
(I think falling within bound upper and lower limits would form a spherical
shell). Actually, I have a cylindrical shell volume consideration and I
should not expect that cpptraj should be able to handle all customized
volume as what user thinks :) But I just wish to know if I am thinking in
right direction or not (pasted as in previous mail): "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."
kind regards,
Jiom
On Mon, Jul 14, 2014 at 4:51 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This totally slipped my mind before, but the 'stfcdiffusion' diffusion
> calculation in CPPTRAJ (contributed by H. Loeffler) may be able to do what
> you want. You can calculated MSD of atoms within a certain distances bounds
> of a second mask, e.g.
>
> stfcdiffusion :WAT.O out diffusion.dat time 1.0 mask2 :7 lower 0.01 upper
> 3.5 nwout numwater.dat
>
> Would calculate MSD for water oxygens that are between 0.01 and 3.5 Ang.
> away from residue 7 (I believe). See the manual or
> http://www.stfc.ac.uk/CSE/randd/cbg/software/43740.aspx for more details.
> This routine may be very slow however, so I would test it on a few frames
> first.
>
> Good luck,
>
> -Dan
>
>
> On Sat, Jul 12, 2014 at 2:54 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > 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
> > > > >> > _______________________________________________
> > > > >> > 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)
> > > > >> _______________________________________________
> > > > >> 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)
> > > _______________________________________________
> > > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 14 2014 - 10:00:02 PDT
