Hi,
I am just wondering if am thinking in right direction or not as I discussed
in previous post. I am copying again here:
"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."
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.
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?
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
Received on Sat Jul 12 2014 - 09:30:03 PDT
