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On 20/10/2011 12:26 AM, mu xiaojia wrote:
<blockquote
cite="mid:CABSFTFoz=5QueoaomHTks8je+pQN713v41cP5y4KuwHGvjLFzA@mail.gmail.com"
type="cite">
<div>Dear GMX-users,</div>
<div><br>
</div>
<div>I found a question in 2009 asking which format of improper
does OPLS dihedral gromacs use. I have the same question, is it
periodic or harmonic?</div>
</blockquote>
<br>
The quote below clearly says they are implemented as proper periodic
dihedrals.<br>
<br>
<blockquote
cite="mid:CABSFTFoz=5QueoaomHTks8je+pQN713v41cP5y4KuwHGvjLFzA@mail.gmail.com"
type="cite">
<div>If it is periodic, why in its ffbonded.itp file: <span
class="Apple-style-span" style="font-family: monospace;
white-space: pre; font-size: medium; ">#define
improper_O_C_X_Y 180.0 43.93200 2 what do they mean?</span></div>
</blockquote>
<br>
These defined macros are used in the .rtp file, as your quote says.
See <a
href="http://en.wikipedia.org/wiki/C_preprocessor#Macro_definition_and_expansion">http://en.wikipedia.org/wiki/C_preprocessor#Macro_definition_and_expansion</a>.
The types of numbers and their order match that for dihedral type 1
or 4, which are periodic. If they matched some other order then
another dihedral type would be implied - though this is admittedly a
bit perverse. See table 5.5. in the manual.<br>
<br>
<blockquote
cite="mid:CABSFTFoz=5QueoaomHTks8je+pQN713v41cP5y4KuwHGvjLFzA@mail.gmail.com"
type="cite">
<div><font class="Apple-style-span" face="monospace" size="3"><span
class="Apple-style-span" style="white-space: pre;">Also,
when I plug in tinker's improper dihedrals(which should be
harmonic) into gromacs, the results matches well whith each
other(tinker and gromacs). Does it suggest that gromacs uses
a periodic dihedral?</span></font></div>
</blockquote>
<br>
The quote you make below confirms this.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABSFTFoz=5QueoaomHTks8je+pQN713v41cP5y4KuwHGvjLFzA@mail.gmail.com"
type="cite">
<div><span class="Apple-style-span" style="font-family: monospace;
white-space: pre; font-size: medium; "><br>
</span></div>
<div><span class="Apple-style-span" style="font-family: monospace;
white-space: pre; font-size: medium; ">Thanks, here is the
part I quoted from ffbonded.itp</span></div>
<div><br>
</div>
<div>[ dihedraltypes ]</div>
<div>; Improper OPLS dihedrals to keep groups planar.</div>
<div>; (OPLS doesnt use impropers for chiral atoms).</div>
<div>; Since these functions are periodic of the form 1-cos(2*x),
they are actually</div>
<div>; implemented as proper dihedrals [1+cos(2*x+180)] for the
moment,</div>
<div>; to keep things compatible.</div>
<div>; The defines are used in ffoplsaa.rtp or directly in your
.top file.</div>
<div><br>
</div>
<div>--jia</div>
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