<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
On 4/28/2011 1:54 PM, Sanku M wrote:
<blockquote cite="mid:766169.25636.qm@web114219.mail.gq1.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div style="font-family: 'times new roman','new york',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>
Sure, you need as many constraints as <a
href="http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29">http://en.wikipedia.org/wiki/Degrees_of_freedom_(physics_and_chemistry)</a><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 cite="mid:766169.25636.qm@web114219.mail.gq1.yahoo.com"
type="cite">
<div style="font-family: 'times new roman','new york',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 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 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>
-- gmx-users mailing list <a moz-do-not-send="true"
ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<span><a moz-do-not-send="true" target="_blank"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br>
<span>Please search the archive at <a
moz-do-not-send="true" target="_blank"
href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!</span><br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
ymailto="mailto:gmx-users-request@gromacs.org"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
<span>Can't post? Read <a moz-do-not-send="true"
target="_blank"
href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br>
</div>
</div>
</div>
</blockquote>
<br>
</body>
</html>