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

[Kukol, Andreas]

I am not sure about your workaround, how to shift something.
The updated topology contains the correct potential phi2 as described in the publication, but it is expressed with Ryckaert-Bellemans potentials.

Andreas

-----------------------

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Alex Smolyanitsky
Sent: 03 May 2010 21:32
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

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
--
gmx-users mailing list    gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--
gmx-users mailing list    gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org<mailto:gmx-users-request at gromacs.org>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php