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On 5/11/2010 6:36 AM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTi=ZCa=7ZLyy7GAz6vy+PrfxpYnrrWtJZdZ1=C8m@mail.gmail.com"
type="cite">Thanks Justin. I was just making sure that I was
modifying the relevant files. <br>
</blockquote>
<br>
You can verify things for yourself by making a .tpr, making the
change, making the new .tpr and then using gmxcheck to compare the
two.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=ZCa=7ZLyy7GAz6vy+PrfxpYnrrWtJZdZ1=C8m@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Thu, Nov 4, 2010 at 2:17 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">When using the charmm forcefield, the
following is the case:<br>
1. ffnonbonded.itp - has listed paramters for tip3p (and
other water models) OWT3 and HWT3<br>
2. ffbonded.itp - does not have paramters for OWT3 and
HWT3<br>
Does this mean:<br>
1. nonbonded parameters for tip3p are read from
ffnonbonded.itp for ALL nonbonded interactions OR<br>
for water-water interactions are read from tip3p.itp file
and for protein-water are read from ffnonbonded.itp?<br>
<br>
</blockquote>
<br>
</div>
Nonbonded interactions are applied uniformly, unless they are
modified in a specific [nonbond_params] directive. Isn't this
something we've worked through before?<br>
<br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html</a>
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">2.bonded paramters for tip3p are read from
tip3p.itp file?<br>
<br>
</blockquote>
<br>
</div>
Bonded parameters for water models are really only relevant if
using a flexible model (which you shouldn't). Otherwise, the
SETTLE algorithm simply fixes the geometry. This is all
determined by the #ifdef FLEXIBLE statement in, for instance,
tip3p.itp.<br>
<br>
-Justin
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">Pooja<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</blockquote>
<br>
</div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu/"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</blockquote>
<br>
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