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<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 lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Matteus
Lindgren <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Graduate
student <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Department
of Chemistry<br>
Umeċ University<br>
SE-901 87 Umeċ, 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>
<br>
</span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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