Oops..., indeed, Gromos was parameterized for use with 1.4 nm :S<br>Should also have checked my sources first. Scuziscuziscuzi...<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;">
Thanks Tsjerk,<br><br>but what about the following gromacs page:<br><a href="http://www.gromacs.org/blogcategory/page_4.html">http://www.gromacs.org/blogcategory/page_4.html</a><br>and the following article of van Gunsteren
<br>"J Comp Chem, 1998, 19:535" which suggests the use of 1.4 nm?<br><br>Thanks<br>Isabella<br><br>On Wed, 21 Jun 2006, Tsjerk Wassenaar wrote:<br><br>> Hi Isabella,<br>><br>> The Gromos force fields were parameterized for use with a rvdw cutoff of
0.9.<br>> Other cutoffs may introduce artefacts.<br>><br>> Ciao!<br>><br>> Tsjerk<br>><br>> On 6/21/06, Isabella Daidone <<a href="mailto:i.daidone@caspur.it">i.daidone@caspur.it</a>> wrote:<br>
>><br>>> 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<br>>> 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>>> _______________________________________________<br>>> gmx-users mailing list
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</a><br>>><br>><br>><br>><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>> Nijenborgh 4<br>> 9747AG Groningen, The Netherlands<br>> +31 50 363 4336<br>><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</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>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>