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On 4/28/2011 7:07 PM, Sanku M wrote:
<blockquote cite="mid:353666.31166.qm@web114218.mail.gq1.yahoo.com"
type="cite">
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<div style="font-family: 'times new roman','new york',times,serif;
font-size: 12pt;">
<div>Thanks Mark for your comment. But, as far as degrees of
freedom is concerned, if there is a tetrahedral molecule as I
shown below with atom #1 ( B) being center of the tetrahedron
, if we had defined the molecules in terms of bonds and angles
( in stead of constraints ), we would have 4 bonds (
1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5
, 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors
.</div>
</div>
</blockquote>
<br>
Different things happen in each case. A redundant but consistent
bonded interaction adds (at most) a small contribution to the
energies and forces. Consider what the effect of a
suitably-constructed H-H-C angle function of a methylene in an
equilibrium configuration would be... nothing significant.<br>
<br>
However, an implementation of coupled constraints so that they are
all mutually satisifed in few iterations is hard enough without
having to cope with redundancy also.<br>
<br>
<blockquote cite="mid:353666.31166.qm@web114218.mail.gq1.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new york',times,serif;
font-size: 12pt;">
<div>In that case, the simulation goes fine . But, then wonder,
why, for constraints, we can put only 9 descriptors . </div>
<div>Also, I have tried all possible combination to get 9
constraints, but , in each case, gromacs crashes. However,
defining 4 bonds and 6 angles using high force-constant lets
the simulation go fine. So, on a second thought, I wonder
whether defining 9 bond-constraints to get a stable
tetrahedral molecule is at all possible. </div>
</div>
</blockquote>
<br>
So you need to read the LINCS and/or SHAKE literature :-) You say
these other codes can do rigid-body simulations, so there must be
literature on how to do it.<br>
<br>
<blockquote cite="mid:353666.31166.qm@web114218.mail.gq1.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new york',times,serif;
font-size: 12pt;">
<div>Do I need to go for some sort of compromise, where 4 bonds
( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles
with high force-constant are defined to maintain tetrahedral
nature ? <br>
</div>
</div>
</blockquote>
<br>
Maybe.<br>
<br>
<blockquote cite="mid:353666.31166.qm@web114218.mail.gq1.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new york',times,serif;
font-size: 12pt;">
<div>I am not sure what should be the best possible 9
constraints . <br>
</div>
</div>
</blockquote>
<br>
Don't know. I would start trying four B-F bonds and five F-F bonds,
but it shouldn't matter.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:353666.31166.qm@web114218.mail.gq1.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new york',times,serif;
font-size: 12pt;">
<div> <span class="Apple-style-span"
style="font-family: times,serif;"> 1 opls_1014 1 BF4
B 1 0.8276</span></div>
<blockquote type="cite">
<div style="font-family: times,serif; font-size: 12pt;">
<div style="font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">
<div style="font-family: 'times new roman','new
york',times,serif; font-size: 12pt;">
<blockquote type="cite">
<div style="font-family: times,serif; font-size:
12pt;">
<div> 2 opls_1015 1 BF4 F1 1
-0.4569</div>
<div> 3 opls_1015 1 BF4 F2 1
-0.4569</div>
<div> 4 opls_1015 1 BF4 F3 1
-0.4569</div>
<div> 5 opls_1015 1 BF4 F4 1
-0.4569</div>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;"><br>
<div style="font-family: times new roman,new york,times,serif;
font-size: 12pt;"><font face="Tahoma" size="2">
<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
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<b><span style="font-weight: bold;">Sent:</span></b> Thu,
April 28, 2011 1:00:42 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] rigid tetrahedral molecule<br>
</font><br>
On 4/28/2011 3:49 PM, Sanku M wrote:
<blockquote type="cite">
<div style="font-family: times,serif; font-size: 12pt;">
<div> I went through the LINCS manual . But, I am still
struggling with coming up with the idea of putting
correct constraint to maintain the rigidity of
tetrahedral molecule . I seem to understand from
your suggestion that the tetrahedral can be seen as a
combination of 4 coupled triangles.( or am I still
wrong about it ?)</div>
</div>
</blockquote>
<br>
I think it's seven coupled triangles, but that's not a
relevant way to think about it. You have 5 atoms, so 3N-6
means 9 degrees of freedom, so you need 9 independent
descriptors of relative atomic positions, so 9 constraints.
You were trying 10 and 5.<br>
<br>
Because those constraints form triangles, you may need to
take care with LINCS to get a stable simulation. Read up on
the details here, I don't remember them.<br>
<br>
<blockquote type="cite">
<div style="font-family: times,serif; font-size: 12pt;">
<div>In that case, am I supposed to use multiple settle
to keep the molecule in a tetrahedral fashion ? I am
sorry but if you can explain it in bit more details, I
might get the point.</div>
</div>
</blockquote>
<br>
Forget about SETTLE - it was just an example to illustrate
that this is not easy to do right. There's a specialised
algorithm for rigid water (with three coupled bond
constraints) because it is fiddly to get such things right
(and fast).<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="font-family: times,serif; font-size: 12pt;">
<div style="font-family: times new roman,new
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<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><font
face="Tahoma" size="2">
<hr size="1"><b><span style="font-weight: bold;">From:</span></b>
Mark Abraham <a moz-do-not-send="true"
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<b><span style="font-weight: bold;">Sent:</span></b>
Wed, April 27, 2011 11:14:34 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] rigid tetrahedral molecule<br>
</font><br>
On 4/28/2011 1:54 PM, Sanku M wrote:
<blockquote type="cite">
<div style="font-family: times,serif; font-size:
12pt;">
<div>Hi,</div>
<div> I tried to keep the geometry of the BF4
fixed by using constraints using lincs. But ,
unfortunately, my simulation is crashing
immediately and if I try minimization with
only 2 molecules, it provides a lot of LINCS
warning and generate a lot of step*.pdb file .
If I try to visualize the minimized snapshot
in VMD, it looks like all the distances I
tried to constrain decreased drastically.
Finally, trying MD run with this "minimized"
configuration results in crashing due to bad
contacts.</div>
<div><br>
</div>
<div> I am sure I am doing something wrong and
it might be that my itp file is wrong . So any
help will be highly appreciated.</div>
<div>Here is the details of what I did.</div>
<div><br>
</div>
<div> The geometry of the molecule is
tetrahedral with B at the center and 4 F atoms
is surrounding it in a tetrahedral manner.</div>
<div>I first generated a itp file for BF4 which
is shown below: I first got the LJ parameters
and charges for B and F atom and put them in
ffoplsnb.itp file as new atom types opls_1014
and opls_1015 . Initially I tried to put
contsraint along all bonds ( i.e among F atoms
as well ). But, grompp provides warning that
number of constraint is more than number of
degrees of freedom. So, I reduced number of
constraints by only putting constraint among B
and F. But, it did not work either. <br>
</div>
</div>
</blockquote>
<br>
<span><span> Sure, you need as many constraints as <a
moz-do-not-send="true" target="_blank"
href="http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29">http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29</a></span></span><br>
<br>
You should also do your homework about using LINCS
and coupled triangles of constraints, as I suggested
last time.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="font-family: times,serif; font-size:
12pt;">
<div>Here is the .itp file I wrote for rigid
BF4 . It will be great if someone can point me
what I am doing wrong.</div>
<div><br>
</div>
<div> [ moleculetype ]</div>
<div>; molname nrexcl</div>
<div>BF4 3</div>
<div><br>
</div>
<div>[ atoms ]</div>
<div>#ifdef _FF_OPLS</div>
<div> 1 opls_1014 1 BF4 B 1
0.8276</div>
<div> 2 opls_1015 1 BF4 F1 1
-0.4569</div>
<div> 3 opls_1015 1 BF4 F2 1
-0.4569</div>
<div> 4 opls_1015 1 BF4 F3 1
-0.4569</div>
<div> 5 opls_1015 1 BF4 F4 1
-0.4569</div>
<div>#endif</div>
<div>[ constraints ]</div>
<div> 1 2 1 0.146</div>
<div> 1 3 1 0.146</div>
<div> 1 4 1 0.146</div>
<div> 1 5 1 0.146</div>
<div> ; 2 3 1 0.238</div>
<div>; 2 4 1 0.238</div>
<div>; 2 5 1 0.238</div>
<div>; 3 4 1 0.238</div>
<div>; 3 5 1 0.238</div>
<div>; 4 5 1 0.238</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><br>
</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">[
exclusions ]</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">1
2 3 4 5</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">2
1 3 4 5</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">3
1 2 4 5</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">4
1 2 3 5</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;">5
1 2 3 4</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><br>
</div>
<div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><br>
</div>
<div style="font-family:
arial,helvetica,sans-serif; font-size:
13px;"><font face="Tahoma" size="2">
<hr size="1"><b><span style="font-weight:
bold;">From:</span></b> Mark Abraham <a
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class="moz-txt-link-rfc2396E"
ymailto="mailto:Mark.Abraham@anu.edu.au"
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<b><span style="font-weight: bold;">Sent:</span></b>
Wed, April 27, 2011 8:39:23 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] rigid tetrahedral molecule<br>
</font><br>
On 4/28/2011 11:25 AM, Justin A. Lemkul
wrote:<br>
> <br>
> <br>
> Sanku M wrote:<br>
>> Hi,<br>
>> I am interested in simulating a
anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which
developed the parameters for this molecule,
it is mentioned that it has been used as
'rigid' molecule i.e the molecule only has
non-bonding interaction but there was no
intramolecular motion as the geometry was
fixed.<br>
>> I am trying to simulate this
molecule in gromacs treating it as rigid.
But, I was looking for best way to
'rigidify' this molecule.<br>
>> <br>
>> I was wondering whether using LINCS
to constrain all B-F and F-F bonds will be
good enough . Or, Should I use virtual
sites ? If I really need to use virtual
site, will it be something like TIP5P water
model ?<br>
>> Can someone suggest the best
wayout ?<br>
>> <br>
> <br>
> Constraints should do the trick, but
probably the best approach is to simply
contact the authors who developed the model
and ask how they did it. Then you know
you're exactly reproducing what they did.<br>
<br>
Yep.<br>
<br>
Be aware that the coupled constraints make
life tricky, and you should read up in the
manual and literature for how best to use
P-LINCS in such cases. Algorithms like
SETTLE for rigid water exist for a reason...<br>
<br>
Mark<br>
<br>
<br>
<br>
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</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
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