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On 4/28/2011 3:49 PM, Sanku M wrote:
<blockquote cite="mid:907400.87119.qm@web114211.mail.gq1.yahoo.com"
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<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>
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<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 cite="mid:907400.87119.qm@web114211.mail.gq1.yahoo.com"
type="cite">
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<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
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<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">
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<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> 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><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>
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<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>
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font-size: 13px;"><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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Discussion list for GROMACS users <a
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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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