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

[Alex Smolyanitsky]

Thanks Andreas.

Is there any difference force-wise between this and our little workaround?

Alex


On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas <a.kukol at herts.ac.uk> wrote:

> Hi,
>
> The POPC_53a6 topology works only with Gromacs versions lower than 4.
> Please find attached the topology compatible with Gromacs4.
>
> I shall update files on the Gromacs website. Sorry for causing confusion.
>
> Best wishes
> Andreas
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On
> Behalf Of Alex Smolyanitsky [asmolya1 at asu.edu]
> Sent: 03 May 2010 18:22
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)
>
> 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<mailto:
> 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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