[gmx-developers] force field reorganization done

[Berk Hess]

David van der Spoel wrote:
> On 1/27/10 2:03 PM, Berk Hess wrote:
>> Hi,
>>
>> I have committed the force field reorganization code and all the force
>> field files to git master.
>>
>> If anyone wants to test, please go ahead and give feedback.
>> This is a critical part of GROMACS and should be well tested.
>>
>> The only thing missing, I think, is updating the Makefile.am in
>> share.top and adding ones
>> in the .ff subdirs.
>
> I've just updated and added stuff to the Makefile.am, now at least one
> can install gromacs. A test with the OPLS ff works, however with
> encads I get:
> Atom type opls_135 (residue ACE) not found in atomtype database
>
> The fact that ACE is not in the database does not concern me, but the
> ref to opls_135 is weird. In the encads.ff files there is no mention
> of opls_135 in any file.
I now fixed this by giving a fatal error by default when a residue entry
is found twice.
The error message gives the hint that you can use the -rtpo option to allow
local rtp files to override entries in the library rtp files.

>
>> Also the manual still needs to be updated.
>>
>> Now we can add the AMBER and CHARMM force fields with proper building
>> block
>> naming support and support for renaming terminal building blocks.
>>
>> I am still thinking if it would be useful to be able to keep the
>> "proper" residue names
>> and not replace them by the building block names. This might not be very
>> useful,
>> because you can no longer easily see the protonation state or special
>> bonds of residues.
>
> In the context of qhop-development we are thinking of having all
> protons on all residues (e.g. two H on a GLU sidechain) and store an
> existence function in the occupancy field of the pdb. Maybe this
> should not be done in general, but some feedback on the idea would be
> appreciated.
I would prefer to have all the force field files only contain
"standard", published parameters and topologies.
But adding a force field is now as simple copying a directory in the
library dir or your working dir.
So force field packages can easily be provided and installed.

Berk
>
>
>>
>> Berk
>>
>
>