[gmx-users] Proper Dih. multiplicity
spoel at xray.bmc.uu.se
Mon Aug 15 21:31:57 CEST 2005
On Mon, 2005-08-15 at 12:34 -0300, Alberto Malvezzi wrote:
> I'm having the same problem described bellow, which is the error message
> Fatal error: [ file "topology_A.itp", line 8909 ]:
> Proper Dih. multiplicity can not be perturbed 6.000000!=3.000000
just add the parameters twice.
> I have read the answer given earlier, and I seem to understand in which file I should define this B topology.
> Any help would be appreciated.
> Hi all.
> />/ I'm trying to simulate a sugar molecule and I have some problems whith proper
> />/ dihedrals (ffgmx) when I try to run grompp.
> />/ I need to define dihedral angles with different multiplicity for the same
> />/ group of atoms. (I don't want to do FEP)
> />/ 1 3 6 9 1 0.0 5.858 3
> />/ 1 3 6 7 1 0.0 0.418 2
> />/ The program displays an error message:
> />/ Fatal error: [ file "./hial.itp", line 205 ]:
> />/ Proper Dih. multiplicity can not be perturbed 3.000000!=2.000000
> This is caused by a dihedral type definition in the forcefield where
> a multiplicity is specified. In your topology you specify a different
> multiplicity, which is OK, except that Gromacs also *always* assigns
> a 'B' topology (which is used for FEP), even if you don't use FEP.
> The parameters for the 'B' topology come from the dihedral type
> definition and not from your topoligy definition. So the solution is
> to explicityly define the 'B' topology so it will be identical to
> the 'A', like:
> 1 3 6 7 1 0.0 0.418 2 0.0
> 0.418 2
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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