SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity

[Sarah Witzke]

Hi again,
 
Thank you very much for your reply Mark. Now, I have a dihedral with the following form:
 
   22    23    24    25     1     0.0   7.47        1 
   22    23    24    25     1     0.0   3.9          2
   22    23    24    25     1  180.0   1.1         3
   22    23    24    25     1     0.0   -2.8425    0

Of course the "problematic" multiplicity of 0 just subtracts 5.685 from the energy. Would it then be OK to simply delete this line? I suppose it would be OK as it just adds a constant to the energy but I'm not 100% certain if it would give any problems with the calculation of forces.
 
Sarah

Sarah Witzke wrote:
> Dear gromacs users,
>
> I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives the following error:
>
> /people/disk2/sarah/gromacs-4.0.3/bin/grompp -f em.mdp -c system.gro -p popcpalc32.top -o test.tpr
>
> Ignoring obsolete mdp entry 'cpp'
> checking input for internal consistency...
> processing topology...
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxnb.itp
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ffgmxbon.itp
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ff_dum.itp
> Generated 1502 of the 2346 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 1068 of the 2346 1-4 parameter combinations
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/flexspc.itp
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/spc.itp
> Opening library file /people/disk2/sarah/gromacs-4.0.3/share/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'PALC'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'POPC'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.3
> Source code file: convparm.c, line: 68
>
> Fatal error:
> Value of 'multiplicity' in Proper Dih. is 0, which is smaller than the minimum of 1
> -------------------------------------------------------
>
> When looking through the lipid .itp file (popc.itp) I do see dihedrals with multiplicity of 0 (which is not the case in dmpc.itp) - I haven't made it myself but it has been used many times before.
>
> When running grompp in version 3.3.3 I get no error message:

Yup - there was no test for validity of the input.

Since a proper dihedral with multiplicity of zero is just a constant
(see manual eq 4.61), it does nothing at all to the forces, nothing
meaningful to energies and nothing to energy differences. Other than a
convenient way to "comment out" dihedrals (which would be better done
with a real comment!) I can't see the purpose of such dihedrals of
multiplicity zero.

Mark
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