[gmx-users] constant term in dihedral potential function

Berk Hess gmx3 at hotmail.com
Fri May 29 09:31:44 CEST 2009

> Date: Fri, 29 May 2009 16:52:50 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] constant term in dihedral potential function
> Kukol, Andreas wrote:
> > Many thanks for your help.
> > 
> > As for the 1-4 interactions, I am using the Gromos53a6 forcefield for everything apart from this particular dihedral.
> > 
> > I did not exclude 1-4 interactions previously with the multiple dihedral terms. Does this mean, if I use Ryckaert-Bellemans now (yielding the same potential function), I don't need to make any changes to 1-4 interactions ?
> > 
> > Note that the previous method has been validated (with Gromacs 3.3), the problem is that it doesn't work with Gromacs 4 anymore. So I am trying to achieve the same result with Ryckaert-Bellemans instead of multiple periodic dihedrals.
> My earlier side point was that you can use multiple periodic dihedrals 
> of type 9 if those dihedrals follow each other directly. Such dihedrals 
> are effectively of type 1 (see code fragment below).
> You still won't get one of multiplicity 0, but such a function doesn't 
> influence the dynamics (dV/dr = 0) and would always cancel out of any 
> energy comparisons you might do. So I don't think it serves a purpose.
> >> I don't believe this works in the way you might expect. Page 109 of the
> >> manual contradicts me, but (undocumented) dihedral type 9 was added
> >> recently to allow multiple strictly-consecutive dihedrals of type "1" to
> >> be accumulated on the same atoms. Anyway, this can readily be checked by
> >> comparing 0-step EM runs, before and after commenting out the last of
> >> the multiple dihedrals pre-grompp. Also, you can look at a gmxdump of
> >> the .tpr.
> > 
> > This works fine.
> I was looking at (4.0.5) src/kernel/toppush.c today for something else, 
> and there's a comment in support of my statement above:
> 	if(ft == 9)
> 	{
> 		/* Previously, we have always overwritten parameters if e.g. a torsion
> 		 with the same atomtypes occurs on multiple lines. However, CHARMM and
> 		 some other force fields specify multiple dihedrals over some bonds,
> 		 including cosines with multiplicity 6 and somethimes even higher.
> 		 Thus, they cannot be represented with Ryckaert-Bellemans terms.
> 		 To add support for these force fields, Dihedral type 4 is identical to
> 		 normal proper dihedrals, but repeated entries are allowed.
> 		 */
> 		bAllowRepeat = TRUE;
> 		ft = 1;
> 	}
> 	else
> 	{
> 		bAllowRepeat = FALSE;
> 	}
> The comment should refer to type 9 iso type 4, of course (and again in 
> the warning text in push_bondtype() in the same source file). Further, 
> push_bondtype() produces a grompp warning about overriding parameters in 
> the other cases. So I think Berk is wrong here. Andreas should have a 
> look at his grompp warnings, perhaps.
> Mark

Indeed the number should be 9 iso 4.

But this is a different issue.
These changes are to enable automatic parameter settings based on atomtypes
for multiple dihedrals over the same bonds.
Andreas specifies the parameters on the same line in the [ dihedrals ] section.
In that case every works (and has alwats worked) fine.


Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090529/e284a6d7/attachment.html>

More information about the gromacs.org_gmx-users mailing list