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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