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

[XAvier Periole]

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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