Rob,<br>
<br>
I'll give you what I've got in terms of documentation, if I can find it
again (Here is the thread, I think:
<a href="http://www.gromacs.org/pipermail/gmx-users/2002-September/002760.html">http://www.gromacs.org/pipermail/gmx-users/2002-September/002760.html</a>).
There are some other remarks related to this elsewhere on the mailing
list but they're a bit hard to find. As you noticed, it's not actually
documented in the manual. (And, when I started using dihedral
restraints in 3.2, that section of code hadn't been actually written
yet, there was just a placeholder which printed out "Dihedral
restraints on," and set the energies to zero). (Another e-mail I got
info from was this one:
<a href="http://www.gromacs.org/pipermail/gmx-users/2004-February/009536.html">http://www.gromacs.org/pipermail/gmx-users/2004-February/009536.html</a>)<br>
<br>
I should also mention that I found a bug in this section of code in
3.3, so you will need the dihres.c file from CVS, or alternatively if
you e-mail me directly I can e-mail you the fixed version. (The bug was
that the energies were right, but the forces were the negative of what
they should have been, meaning that it would make the dihedrals exactly
the opposite of what they should have been. See the bugzilla here:
<a href="http://bugzilla.gromacs.org/show_bug.cgi?id=32">http://bugzilla.gromacs.org/show_bug.cgi?id=32</a>)<br>
<br>
More below.<br><br><div><span class="gmail_quote"><br>
</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>>[ dihedral_restraints ]<br>>;
i j k
l type
label phi dphi kfac power<br>>1410
1393 1391
2610 1 0 -140 0 fc_dihed
2<br>><br>>mdp file:<br>><snip><br>>define = -Dfc_dihed=41.84<br>><snip><br>>dihre=simple<br>>dihre-fc=1<br>><br>>David<br><br>Thanks David. Yes constraint = restraint in my last message. Where do you
<br>find the documentation for the [dihedral_restraints], because i didn't find<br>it in the manual.<br>Just so that i understand it correctly, the restraint is of the form:<br>fc_dihed *(phi-dphi) ^power</blockquote><div>
<br>
Similar to that. There's a factor of 1/2 in front and it's better
written by taking phi'=phi-phi0, then V=fc_dihed/2*(phi-dphi)^power
when phi'>dphi or phi'<-dphi and zero elsewhere (that is, setting
dphi to be nonzero makes it a flat-bottom well of width 2*dphi). </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">so what then is type (1 for proper 2 for improper?!) and what is label?..
<br>and can i define my fc_dihed in my .top file directly? what is the advantage<br>of defining it in the .mdp file<br>what do dihre=simple, and dihre-fc=1 mean? are there any other "keywords"<br>out there?</blockquote>
<div><br>
I really have no idea about the types, sorry. Maybe we can get the
developers to provide some documentation on this. Or you can look at
the source (dihres.c isn't particularly complicated) to see what it's
doing. I did at one point but I don't remember checking to see what the
types do. Maybe if you do so you can send an e-mail to the list for
documentation purposes. :)<br>
<br>
"label", however, I can explain. Like with atoms, you number your
restraints in each section. So label 0 is the first restraint, label 1
the second, etc. <br>
<br>
fc_dihed isn't necessary. You can replace it with numbers in your
topology file, or with a define fc_dihed section in your topology file
if you want. I just had it there for convenience (I was running with a
bunch of different dihedral restraint values for different jobs which
would run at the same time, and didn't want to have to make N different
topology files, so I put the fc_dihed value in my topology file and
then used a define statement in my individual mdp files to set it to
different values for different runs. <br>
<br>
dihre-fc is a multiplier for the force constant value in the topology
file, supposedly, if I remember correctly. I am not sure that it works,
but it might.<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">much appreciated if you can give me a pointer or 2 to the above questions.<br>Thank you very much in advance.
<br><br>rob</blockquote><div><br>
Sorry I can't be of more help. Again, if you dig into these
things more, be sure to send an e-mail back to the list for
documentation purposes. And let me know if you need the dihres.c source
rather than getting the fixed version from CVS.<br>
<br>
David<br>
<br>
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