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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
