I know it's supported.<div><br></div><div>I was just investigating the possibility since I build acpype to create topologies for gromacs, but also it converts from amber to gromacs (like <a href="http://amb2gmx.pl">amb2gmx.pl</a>), and so I was wondering about RB with 6 coefficients since multiple proper dihedrals is only supported for gmx 4.5 and above.</div>
<div><br></div><div>But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be.<br><br></div><div>Thanks,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">
On 31 March 2011 16:08, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi there,<br>
<br>
Since ILDN dihedrals has some parameters with up to periodicity 6, I was<br>
wondering if it's possible to convert it in RB with 6 coefficients. If<br>
so, what would be the formula? For example, for converting the usual<br>
Amber99SB to RB I have:<br>
</blockquote></div>
ILDN is already supported in the latest gromacs releases, by simply using multiple proper dihedrals. Why would you want to change it?<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
if phase in [0, 180]:<br>
<br>
if kPhi > 0: V[period] = 2 * kPhi * cal<br>
<br>
if period == 1:<br>
<br>
C[0] += 0.5 * V[period]<br>
<br>
if phase == 0:<br>
<br>
C[1] -= 0.5 * V[period]<br>
<br>
else:<br>
<br>
C[1] += 0.5 * V[period]<br>
<br>
elif period == 2:<br>
<br>
if phase == 180:<br>
<br>
C[0] += V[period]<br>
<br>
C[2] -= V[period]<br>
<br>
else:<br>
<br>
C[2] += V[period]<br>
<br>
elif period == 3:<br>
<br>
C[0] += 0.5 * V[period]<br>
<br>
if phase == 0:<br>
<br>
C[1] += 1.5 * V[period]<br>
<br>
C[3] -= 2 * V[period]<br>
<br>
else:<br>
<br>
C[1] -= 1.5 * V[period]<br>
<br>
C[3] += 2 * V[period]<br>
<br>
elif period == 4:<br>
<br>
if phase == 180:<br>
<br>
C[2] += 4 * V[period]<br>
<br>
C[4] -= 4 * V[period]<br>
<br>
else:<br>
<br>
C[0] += V[period]<br>
<br>
C[2] -= 4 * V[period]<br>
<br>
C[4] += 4 * V[period]<br>
<br>
<br>
So, as you can see, I can handle up to 4 periods (C[5] is always 0, but<br>
not with ILDN and I need to add C[6] rules as well).<br>
<br>
Any ideas? Many thanks in advance,<br>
<br>
Alan<br>
--<br>
Alan Wilter SOUSA da SILVA, DSc<br>
Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
CB10 1SD, Hinxton, Cambridge, UK<br>
+44 1223 49 4588<br>
<br>
</blockquote>
<br>
<br></div></div>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
</div>