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On 26/02/2011 3:09 AM, Moeed wrote:
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite"><br>
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<div class="im"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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Thank you Mark for your detailed explanation. Sorry if I
am slow in understanding some stuff. I appreciate your
patience. <br>
<br>
1- I have an inquiry about index groups. If I specify all
my solute chains as a whole in one group [all chains]
(including n chains having m atoms each) and calculate
interaction energies between the following:<br>
<br>
[all chains] [all chains]<br>
<br>
[all chains] [all solvent] (group with all solvent atoms)<br>
<br>
[all solvent] [all solvent]<br>
<br>
(so [all chains] is consisting of atoms 1 to m + atom
m+1 to 2m...)<br>
<br>
is there a way to get the same results by defining index
groups as individual chains [chain 1] [chain 2] .. [chain
n]? for example<br>
<br>
[chain 1] [all solvent]<br>
+[chain 2] all solvent]<br>
+ chain 3 ..<br>
<br>
= ? [all chains] [all solvent]<br>
</blockquote>
<br>
</div>
Sure. GROMACS will let you define up to 256 energy groups. You
just need to construct an appropriate index file. You can then
add them together in whatever way suits you, but you'll need
to use some other tool to post-process what g_energy reports.</blockquote>
<div class="im"><br>
I think you answered my question here. If I understand
correctly, say [all chains] [all chains] LJ-SR interaction
energy is the sum of LJ SR with index file of separate chains.
That is:<br>
LJ SR of [chain 1] [chain 1]+<br>
[chain 2] [chain 2]+</div>
</div>
</blockquote>
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div class="im">[chain 3][chain 3]+</div>
<div>.....= [all chains] [all chains] LJ SR <br>
</div>
</div>
</blockquote>
<br>
Not in general. There may be cross terms. LJ SR-[chain 1] [chain 1]
is the sum of the short-range LJ interactions of all pairs of atoms
within the cutoff where both are in chain 1 (ignoring exclusions).
LJ SR-[all chains] [ all chains] is the sum of the short-range LJ
interactions of all pairs of atoms within the cutoff where each
member of the pair can come from *any* chain. For example, if chain
1 is close enough to chain 2, then their atoms will interact. These
will contribute to the RHS of your equation, but not the LHS.<br>
<br>
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite">
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<div>
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<div class="im"> <br>
In other words [all chains] looks at individual chains
([atoms 1 to m] + [atoms (m+1) to 2m] +...) but what it
reports is sum over all individual chains?<br>
</div>
</blockquote>
<div><br>
</div>
<blockquote type="cite">
<div class="im">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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2- The energy units are KJ per mol systems. I think this
unit is not helpful since in literature what we see is
energy of a quantity per mol in usual sense. <br>
</blockquote>
<br>
</div>
What's the "usual sense" in which an energy of a binary
mixture is reported?
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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So my question is how can I get units in mol of particles
for a binary mixture? on the list I read gromacs just
divides energies by avogadros number...Does this mean
there is no way of getting quantities in "mol" for
mixtures?<br>
</blockquote>
<br>
</div>
What energy quantities are measured in "mol"?<br>
See <a moz-do-not-send="true"
href="http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html"
target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg27382.html</a>
for discussion.<br>
</blockquote>
</div>
</blockquote>
<blockquote type="cite">Actually I was referring to the same post :)
By "usual sense" I mean Avogadro number of particles. What I was
trying to say is that, In literature we see thermodynamic
quantities per mol (N_A particles). I dont think they report say
heat of capacity per mole of systems..(what gromcs calculates). </blockquote>
<br>
Thermodynamic tables don't report total energies either. Those are
*extensive* by definition. GROMACS energies are saying that if you
had a mole of such systems, that would have an energy whose
magnitude is that reported by GROMACS. So the actual system has an
energy whose magnitude is smaller by a factor of N_A.<br>
<br>
<blockquote type="cite">We always see experimental data in mole
amount of substance.for pure systems, the values g_energy give
should be divided by nmol (no of particles) to get values per mole
of sunstnce and not system.
</blockquote>
<blockquote type="cite">For a binary mixture or ternary system, can
we do the same thing by dividing by N_A? What I am interested in
is interaction energies between my polymer and solvent. If I
define my all chains as [all chains] and get LJ SR and coulomb SR
for [all chains] [all chains], in order to ba able to compare this
with those reported in literature, I need to divide by N_A?</blockquote>
<br>
I can't say, I've no idea with what you think you can compare this
computed quantity.<br>
<br>
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> </div>
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<div class="im">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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3- If I run a simulation with one chain the interaction
energy is smaller than a system with two chains..in fact
there should be one specific value for interaction of
component A with B independent of system size and number
of particles. This is again a matter of units I think..How
can I calculate the actual energies for a specific system
so that they can be compared with those in literature
(KJ/mol)!<br>
</blockquote>
<br>
</div>
Energies are dependent on system configuration and size. You
have to make sure you are comparing like quantities, e.g. by
normalizing with respect to the number of interacting chains,
or atoms or whatever. I do not understand any sense in which
your assertions above are true.</blockquote>
<div><br>
Tsorry I was not clear with my question..As I mentioned just
above, by normalizing you mean dividing by -nmol? If yes, for
ternary system, I need to divide by N-A oly?<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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4- Again regarding index groups, I am trying to realize
how gromacs deals with a number of chains defined as
awhole in a group [all chains]. For instance for Rg or end
to end distance, what is calculated based on [all chains]
is the average of the case with index file having<br>
[chain 1].... [chain n]?<br>
</blockquote>
<br>
</div>
You can calculate an end-to-end distance of a chain in a
configuration. You can observe the average of that quantity
over a set of configurations. You can compute that average
over different sets of configurations, and average over those
if you want to. But in what sense is the "end-to-end distance
based on [all chains]" meaningful?</blockquote>
<div><br>
By this question I was again trying to realize how
calculations are done by specifying two different index files
( case 1: [all chains] and case 2: [chain 1] [chain 2]...)<br>
<br>
As in question 1 above : for end to end distance does [all
chains] looks at indivdual subchains and takes the average of
Rg or End to end sidtance over chains or it looks at them as a
whole group (a single longer chain containing atoms from atom
number 1 to m*(chain number)..I think my question is clear
now. :) <br>
</div>
</div>
</blockquote>
<br>
If you give GROMACS an operation to do on an index group, it does it
on that index group, not by magically guessing that there are
logical subgroupings. If your operation only makes sense on the
subgroups, do it on them.<br>
<br>
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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In other words [all chains] deals with all chains
separately and reports quantities for ALL the chains as a
group?<br>
</blockquote>
<br>
</div>
If you give a GROMACS tool a set of atoms over which to do an
operation, it does that operation over that set of atoms. If
that operation doesn't make sense on that set of atoms, then
you've asked for a nonsense operation, and the problem does
not lie with GROMACS. </blockquote>
<div> </div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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padding-left: 1ex;">If you want the average of the end-to-end
distance of all your chains over your simulation, then you'll
have to compute the time-average for each chain individually,
and then take the chain-average of them.<br>
</blockquote>
<div><br>
I am sorry Mark but I still dont see this. From what you said
here I understand that specifying [all chains] does not give
average of the case with index file with [chain 1] [chain 2]</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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...<br>
</blockquote>
<div>I thought in the case of interaction energies (question 1
above), gromcas looks at individual chains and adds up
energies:<br>
<br>
[chain 1] [all solvent]<br>
+[chain 2] all solvent]<br>
+ chain 3 ..<br>
<br>
= ? [all chains] [all solvent]<br>
</div>
</div>
</blockquote>
<br>
No. See above. You asked for an operation to be done on the group
[all chains]. It's done on the group [all chains]. It's up to you to
ask for atomic operations. <br>
<br>
The Rg of [all chains] is the radius of gyration of the set of every
atom in [all chains]. That's an atomic operation, but it may well
not be what you what to calculate. If what you want is the average
of Rg over all the chains, then you need to compute Rg for each
chain (an atomic operation), and average it separately.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTikp2OK+pV6RNUnKghCCODakdB4WCjoZ_yDM3RRy@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>Thank you for your time,<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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Mark<br>
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<br>
<br clear="all">
<br>
-- <br>
Moeed Shahamat<br>
Graduate Student (Materials Modeling Research Group)<br>
McGill University- Department of Chemical Engineering<br>
Montreal, Quebec H3A 2B2, Canada<br>
Web:<a moz-do-not-send="true"
href="http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>
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