<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style>
</head>
<body class='hmmessage'>
Hi,<br><br>That depends.<br>If you have explicit parameters in the dihedral section then 1 and 9 are equivalent.<br>If grompp has to look up parameters in the dihderaltypes section there will be difference<br>when multiple parameter lines are present the same atom types for a dihedral type 9.<br><br>Berk<br><br><hr id="stopSpelling">From: alanwilter@gmail.com<br>Date: Fri, 20 Aug 2010 14:41:33 +0100<br>To: gmx-users@gromacs.org<br>CC: gportella@mmb.pcb.ub.es<br>Subject: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber<br><br>Hi there,<div><br></div><div>Now I have some results that I hope to clear this matter about dihe funct 4 and 9 (specially the latter).</div><div><br></div><div>Please see:</div><div><br></div><div><a href="http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx" target="_blank">http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx</a></div>
<div><br></div><div>From my understanding (and results), where dihe funct 4 or 9, replacing both with 1 changes nothing in tot pot energy for amber force fields.<br></div><div><br></div><div>I don't know about charmm here, but I thought amber dihe parameters were sort multiple terms and as far as I remember, the need to convert proper dihe to RBs was necessary for early versions of gromacs 3.x, am I right?</div>
<div><br></div><div>Best,</div><div><br></div><div>Alan</div><div><br><div class="ecxgmail_quote">On 18 August 2010 22:01, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="ecxgmail_quote"><div>Hi Berk and Mark,</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Erik was too lazy to document this, I now added it to the manual.<br></blockquote><div><br></div><div>Is this manual available even via git? When funct 4 and 9 appeared? in gmx 4.5?</div><div><br></div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Type 4 is identical to type 1, it is only there to distinguish improper from proper dihedrals.<br>
</blockquote><div><br></div><div>So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF generated ligand it would do the same thing, right? I ask that for the grace of compatibility with gmx 4.0.x.</div><div>
<br></div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Type 9 is identical to type 1, except that multiple entries in dihedraltypes will lead to<br>
multiple functions on one dihedral.<br></blockquote><div><br></div><div>This one is more difficult to get. I know about multiple entries in CNS, Charmm and Amber. I was even trying to convert amber99bsc0 new dih parameters to gromacs and I was using funct 1. However I didn't have Amber to validate, and now I have Amber11, I don't have time for the moment.</div>
<div><br></div><div>Sounds like funct 9 is to not only pave the way for Charmm, but may help to address properly the bsc0 parameters, right?</div><div><br></div><div>But I need to understand this better. Converting amber's proper dih. param. to gromacs 4.0.x was done by making these dih. to be RB. However <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> converts everything to proper (using funct 1) -- acpype is smarter here. So in gmx 4.0.x proper dih. funct 1 was never able to interpret multiple entries on one dihedral?</div>
<div> </div><div>Now on Mark:</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git commit a7c597c778351f by Erik, whose message was<br>
<br>
Added support for dihedraltype 9, which allows multiple terms for proper dihedrals.<br>
By listing a dihedral with type 9, grompp will now scan the force field to see if there are<br>
multiple terms on _adjacent_ lines listed in the dihedraltypes section, and in that case add them all.<br>
<br>
A code snippet in src/kernel/toppush.c reads<br>
<br>
if(ft == 9)<br>
{<br>
/* Previously, we have always overwritten parameters if e.g. a torsion<br>
with the same atomtypes occurs on multiple lines. However, CHARMM and<br>
some other force fields specify multiple dihedrals over some bonds,<br>
including cosines with multiplicity 6 and somethimes even higher.<br>
Thus, they cannot be represented with Ryckaert-Bellemans terms.<br>
To add support for these force fields, Dihedral type 9 is identical to<br>
normal proper dihedrals, but repeated entries are allowed.<br>
*/<br>
bAllowRepeat = TRUE;<br>
ft = 1;<br>
}<br></blockquote><div><br></div><div>So <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> never worked properly here? For example, I have this for DNA with amber99bsc0:</div><div><br></div><div><span style="font-family: arial,sans-serif; font-size: 13px; border-collapse: collapse; white-space: pre-wrap;"><div><br><br><br>; treated as usual propers in GROMACS since Phase angle diff from 0 or 180 degrees</div><div>; i j k l func phase kd pn</div><div> 2 3 6 23 1 190.98 4.92892 1 ; O5'- C5'- C4'- C3'</div><br><br><br><div> 2 3 6 23 1 295.63 0.38535 2 ; O5'- C5'- C4'- C3'</div><div> 2 3 6 23 1 348.10 4.02848 3 ; O5'- C5'- C4'- C3'</div><div> 28 29 32 33 1 31.80 0.77480 1 ; O3'- P- O5'- C5'</div><br><br><br><div> 28 29 32 33 1 351.96 5.25733 2 ; O3'- P- O5'- C5'</div><div> 28 29 32 33 1 357.25 1.48473 3 ; O3'- P- O5'- C5'</div><div><br></div></span></div><div>
So, this would only work if funct was 9 and not 1 as above? The way it is, the last line of a sequence dih. is overwriting the 2 previous one, ignoring them completely?</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
>From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it can be seen that dihedraltypes 4 and 1 call the same evaluation function. Perhaps Erik can confirm this.<br>
<br>
src/gmxlib/ifunc.c did suggest to me that something is not quite right...<br>
<br>
def_bonded ("PDIHS", "Proper Dih.", 4, 3, 3, eNR_PROPER, pdihs ),<br>
def_bonded ("RBDIHS", "Ryckaert-Bell.", 4, 6, 6, eNR_RB, rbdihs ),<br>
def_bonded ("FOURDIHS", "Fourier Dih.", 4, 4, 4, eNR_FOURDIH, rbdihs ),<br>
def_bonded ("IDIHS", "Improper Dih.", 4, 2, 2, eNR_IMPROPER,idihs ),<br>
def_bonded ("PIDIHS", "Improper Dih.", 4, 3, 3, eNR_PROPER, pdihs ),<br>
<br>
If PIDIHS is an improper dihedral with the functional form of a proper dihedral, should it not use eNR_IMPROPER?<br></blockquote><div><br></div><div><div>I definitely need to run my validations myself, but any words here would be helpful.</div>
</div><div> </div></div>Many thanks you all.<div><br></div><div>Cheers,</div><div><br></div><div>Alan<br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>
80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>
</blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>
<br>--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php </body>
</html>