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On 28/10/2010 3:03 AM, Sai Pooja wrote:
<blockquote
cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
type="cite">
<div>Hi Mark,</div>
<div> </div>
<div>I am familiar with the section, however, I have a few doubts.</div>
<div> </div>
<div>When you say ...</div>
<div>So modified protein-water VDW interactions can be introduced
by defining all relevant "protein atom"-"TIP3P oxygen"
[nonbond_params] terms.</div>
<div>Do you mean that I can introduce [pairtypes] specifying
interactions of all "relevant protein atoms" with "tip3p atoms"?</div>
</blockquote>
No, [pairtypes] are not relevant.<br>
<blockquote
cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
type="cite">
<div> </div>
<div> </div>
<div>and I do not understand - It may be simpler to modify the
[atomtypes] to generate the "modified" VDW from the combination
rule</div>
<div>Would this not alter all non-bonded interactions for the
atomtypes defined? I think I haven't understood thsi properly...</div>
</blockquote>
<br>
I was thinking of a flawed procedure. Ignore this part.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTi=A-NLhULdJh=uE4to72gyGi=aQXzBterkkkABT@mail.gmail.com"
type="cite">
<div> </div>
<div> </div>
<div>Pooja</div>
<div><br>
</div>
<div class="gmail_quote">On Tue, Oct 26, 2010 at 8:21 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="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">I think manual 5.3.3 covers the relevant points.
Let me know what is not clear.<br>
<font color="#888888"><br>
Mark</font>
<div><br>
<br>
----- Original Message -----<br>
From: Sai Pooja <<a moz-do-not-send="true"
href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br>
</div>
<div>
<div>Date: Wednesday, October 27, 2010 9:41<br>
Subject: Re: [gmx-users] Forcefield parameters<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font><br>
<div class="gmail_quote"><font style="font-weight: normal;
font-size: 14px; font-style: normal; background-color:
rgb(245, 248, 240);">> </font>On Tue, Oct 26, 2010
at 6:04 PM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true">mark.abraham@anu.edu.au</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><font style="font-weight: normal; font-size:
14px; font-style: normal; background-color:
rgb(245, 248, 240);">> </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>----- Original Message
-----<br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>From: Sai Pooja <<a
moz-do-not-send="true">saipooja@gmail.com</a>><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>Date: Wednesday, October
27, 2010 8:52<br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>Subject: Re: [gmx-users]
Forcefield parameters<br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>To: Discussion list for
GROMACS users <<a moz-do-not-send="true">gmx-users@gromacs.org</a>><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font><br>
<div class="gmail_quote"><font style="font-weight:
normal; font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>> </font>On Tue,
Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true">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);"><font style="font-weight: normal;
font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size: 14px;
font-style: normal; background-color:
rgb(245, 248, 240);">> </font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal; background-color:
rgb(245, 248, 240);"><font style="font-weight:
normal; font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal; background-color:
rgb(245, 248, 240);"><font style="font-weight:
normal; font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font>Sai Pooja wrote:
<div><br>
<blockquote class="gmail_quote"
style="padding-left: 1ex; margin: 0px 0px
0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);"><font style="font-weight:
normal; font-size: 14px; font-style:
normal; background-color: rgb(245, 248,
240);"><font style="font-weight: normal;
font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font>On Tue, Oct 26, 2010
at 3:46 PM, Justin A. Lemkul <<a
moz-do-not-send="true">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true">jalemkul@vt.edu</a>>>
wrote:<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> Sai Pooja wrote:<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> Hi,<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> I want to
change the non-bonded parameters to modify
the<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> interaction
between water molecules and protein
molecules.<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> I am using
CHARMM forcefield with Tip3p water.<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> The
ffnonbonded.itp file of the forcefield has
non-bonded<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> parameters for
tip3p water. Can I achieve the above by
changing<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> these
parameters?<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> <br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> That depends on
your definition of "modify," but yes, in a
way, you<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> can make changes
here. <br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> 1) Modify - Multiply
sigma and epsilon by a constant<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> If yes, will
this also change the non-bonded parameters
for<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> water - water
interaction?<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font>2) Is there a way to
add a new ifdef perhaps such that a modified
sigma and epsilon can be used for
water-protein interactions and the
unmodified parameters can be used for
water-water interactions?<br>
<font style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font> <br>
</blockquote>
<font style="font-weight: normal; font-size:
14px; font-style: normal; background-color:
rgb(245, 248, 240);"><font
style="font-weight: normal; font-size:
14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font><br>
</div>
<font style="font-weight: normal; font-size:
14px; font-style: normal; background-color:
rgb(245, 248, 240);"><font style="font-weight:
normal; font-size: 14px; font-style: normal;
background-color: rgb(245, 248, 240);">>
</font>> </font>Nonbonded interactions are
calculated during the simulation by applying the
combination rules defined by the force field.
There is no simple way to do this with an
ifdef, since that is just in the topology. You
can't conditionally apply nonbonded parameters.
That just sounds like a recipe for breaking a
force field.<br>
</blockquote>
</div>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font><br>
</div>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font>Not quite right. Parameters for
VDW are calculated from the combination rules from the
atom-specific values given in [atomtypes] only as a
last resort. [nonbond_params] are used in preference
to such.<br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font>So modified protein-water VDW
interactions can be introduced by defining all
relevant "protein atom"-"TIP3P oxygen"
[nonbond_params] terms. It may be simpler to modify
the [atomtypes] to generate the "modified" VDW from
the combination rule, and introduce the "normal" TIP3P
oxygen-oxygen interaction via [nonbond_params].<br>
</blockquote>
<div><font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font> </div>
<div><font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font>Mark, could you please elaborate
the method?</div>
<blockquote class="gmail_quote" style="padding-left:
1ex; margin: 0px 0px 0px 0.8ex; border-left: 1px solid
rgb(204, 204, 204);"><font color="#888888"><font
style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245,
248, 240);">> </font>Mark </font><br>
<font style="font-weight: normal; font-size: 14px;
font-style: normal; background-color: rgb(245, 248,
240);">> </font>--<br>
<font style="font-weight: normal; font-size: 14px;
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