Hi Isabella,<br><br>The Gromos force fields were parameterized for use with a rvdw cutoff of 0.9. Other cutoffs may introduce artefacts.<br><br>Ciao!<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 6/21/06, <b class="gmail_sendername">
Isabella Daidone</b> <<a href="mailto:i.daidone@caspur.it">i.daidone@caspur.it</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sorry, but I'm a little bit confused about what rvdw to use for<br>simulations of proteins in solution with gromos96 force field while using pme for<br>coulomb interactions.<br>In the gromacs 3.3 manual I still read (with pme):
<br>rcoulomb=rlist=rvdw=0.9 nm<br><br>Then, I found in the discussion list (+ the paper J Comp Chem,<br>1998, 19:535) someone suggesting rvdw=1.4 nm.<br><br>Could you please help me? what's your suggestion?<br>Is it nowadays anyway accepted to
<br>use rcoulomb=rlist=rvdw=0.9 nm?<br>And is there any difference between the standard G43a1 version or the<br>newest (G53a...)?<br><br>Thank you very much.<br><br>Isabella<br><br><br><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
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