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Hi Matteus,<br>
<br>
<div align="justify">The time step should be smaller than the fastest
fluctuations in your system, which are normally X-H bonds, with
frequencies around 10fs. To be ten times faster, you should use 1fs,
which normally gives stable simulations even if you don't use
constraints. If you constrain the X-H bonds, you get a factor of two
more-or-less, so you're fine with 2fs. To be on the safe side, you can
constrain all-bonds. More elaborate methods allow you to use a larger
timestep. IIRC, one of David's lectures in the GMX workshop in Finland
had a slide about it, so you can check
<a class="moz-txt-link-freetext" href="http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007/index_html">http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007/index_html</a>
if you're interested.<br>
</div>
<span id="btAsinTitle" style=""><br>
Good luck,<br>
Ran.<br>
<br>
</span>Matteus Lindgren wrote:
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<div class="Section1">
<p class="MsoNormal">Hi all<o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">I´m new to gromacs, having
previously
worked with Charmm. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">After looking through
articles and gromacs
tutorials it seems many use the SETTLE algorithm for water, restraining
both
water angle and bonds, as well as restraining all bonds in proteins,
while
using a timestep of 2fs. I believe in Charmm it is common practice to
only use
SHAKE on X-H bonds, not angles or X-X bonds, for the same timestep. I
got
curious, why the different setups for the different programs, force
fields? <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I will be running protein in
explicit water
simulations and need a timestep of 2fs. Forces and energies in the
system will
be analyzed. What restraint setup should I choose?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Regards<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/Matteus <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">Matteus
Lindgren <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">Graduate
student <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">Department
of Chemistry<br>
Umeå University<br>
SE-901 87 Umeå, Sweden<br>
Tel: +46 (0)90 786 53 68<br>
e-mail: <a href="mailto:barbara.addario@chem.umu.se"><span
style="color: blue;">matteus.lindgren@chem.umu.se</span></a><br>
</span></p>
</div>
</blockquote>
<br>
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