[gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are
concerned, these dihedrals can be commented out. When considering the energy
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole <x.periole at rug.nl> wrote:

>
> HAve look at the paper describing the topology ...
>
>
>   On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:
>
>   Hello everyone,
>
> I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies) for a simple lipid in water sim (gromacs version 4.0.5).
>
> I am using the lipid coordinates from the same archive and here's my
> topology:
> ***
> #include "ffG53a6.itp"
> #include "popc_53a6.itp"
> #include "spc.itp"
>
> [ system ]
> ;Name
> test
>
> [ molecules ]
> POPC      128
> SOL       3585
> ***
>
> grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
> which is smaller than the minimum of 1" without any prior warnings.
> The error has to do with two dihedral angles with zero multiplicity:
>
> ...
> 22   23   24   25   1   90   -5.685   0
> ...
> 24   25   26   27   1   90   -5.685   0
> ...
>
> So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
> have zero equilibrium angle and a multiplicity of 3:
>
>  ...
> 22   23   24   25   1   0.0   5.858   3
> ...
> 24   25   26   27   1   0.0   5.858   3
> ...
>
> Did the author of the 53a6 topology want to simply remove these dihedrals
> by setting a multiplicity of zero? Or, should these two be set according to
> the older topology? I know similar questions have been asked here in the
> past, but I really want to make sure my topology is sane. Thanks a lot.
>
> Alex
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