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On 4/20/2011 4:14 AM, Sikandar Mashayak wrote:
<blockquote
cite="mid:BANLkTinVGJ5DgxcbZyUod1x5FrzXPsqABA@mail.gmail.com"
type="cite">I just did 2 tests in first I do md rerun with SOL SOL
exclusions along with PME option then I get forces on water atoms
but in second case when I use Cut-Off for electrostatic forces are
zero... not sure why PME introduces forces despite using energy
exclusion group...<br>
</blockquote>
<br>
Because that's how PME works. Part of the electrostatic non-bonded
contribution is done in reciprocal space, and that can't be readily
decomposed into group-wise contributions.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTinVGJ5DgxcbZyUod1x5FrzXPsqABA@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Tue, Apr 19, 2011 at 11:39 AM,
Sikandar Mashayak <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:symashayak@gmail.com">symashayak@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Also, in the case of spc/e bulk water when I do md rerun with
SOL SOL exlcusion I see forces on water atoms, however I was
expecting it to be zero.
<div>
<div class="h5"><br>
<br>
<div class="gmail_quote">On Tue, Apr 19, 2011 at 11:12 AM,
Sikandar Mashayak <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">Yes, 7.3.19 says that all
non-nonbonded interactions are excluded within
energy_exclusion groups.
<div><br>
</div>
<div>What I really trying is to get forces on water
atoms only because of water water interactions and I
want force on protein atoms to be zero, so I do md
rerun with energy_exclusion as PROTEIN PROTEIN
PROTEIN SOL and also remove any bond interaction
information from .top file for protein, but still I
get force values on protein atoms. Not sure whats
going wrong?</div>
<div><br>
</div>
<div>thanks</div>
<div>sikandar
<div>
<div><br>
<br>
<div class="gmail_quote">On Tue, Apr 19, 2011 at
12:04 AM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:
0pt 0pt 0pt 0.8ex; border-left: 1px solid
rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<div> On 4/19/2011 2:57 PM, Sikandar
Mashayak wrote:
<blockquote type="cite">so that means if
I define a index group GRP and energy
exclusion GRP GRP then all the
non-boned interactions between atoms
belonging to GRP group are excluded?<br>
</blockquote>
<br>
</div>
What does manual 7.3.19 say?<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">On Mon, Apr
18, 2011 at 7:43 PM, Mark Abraham
<span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid
rgb(204, 204, 204);
padding-left: 1ex;">
<div text="#000000"
bgcolor="#ffffff">
<div> On 4/18/2011 1:43 PM,
Sikandar Mashayak wrote:
<blockquote type="cite">Also,
what about non-bonded
interactions within the
protein? Does exclusion
group only exclude the
non-bonded interactions
between two different
molecules and non-bonded
interactions within the
single molecule atoms are
still computed?<br>
</blockquote>
<br>
</div>
The sets of atoms for energy
groups and such exclusions are
defined by the index groups,
not molecules. See manual 7.3
and wherever it talks about
groups in an early chapter.
<div><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">On
Sun, Apr 17, 2011 at
10:38 PM, Sikandar
Mashayak <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin: 0pt 0pt
0pt 0.8ex;
border-left: 1px solid
rgb(204, 204, 204);
padding-left: 1ex;">
Hi
<div><br>
</div>
<div>When we define
energy group
exclusions e.g. like
in manual <span
style="font-size:
12px; font-family:
Helvetica;">energygrp
excl = Protein
Protein SOL SOL </span></div>
<div><font
face="Helvetica">and
do md rerun, then
only non-bonded
interactions
between Protein
and SOL are
computed. I am
wondering what
happens to bonded
interactions
within the
protein, do they
contribute to
energies even
though we have
excluded
protein-protein
interactions?</font></div>
</blockquote>
</div>
</blockquote>
<br>
</div>
Bonded interactions are
unaffected, as you will see if
you try it.<br>
<br>
Mark<br>
<br>
</div>
<br>
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