R: R: [gmx-users] Dihedral restraints

[Yang Ye]

You may consider to use following to get the latest 3.3.

cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co -r 
release-3-3-patches gmx

Yang Ye

STEVENAZZI ANDREA wrote:
> Dear David
> I am desperate actually and would appreciate a lot if you could send me the dihres.c that works with version 3.2.
> Just in case is not so clear how to add the right lines in the topology file by reading the code would you please suggest it to me too?
> Thanks a lot
> Best regards
> Andrea
>
>
> Andrea Stevenazzi
> Medicinal & Computer Chemistry
> Italfarmaco Research Centre
> Italfarmaco SpA
> Via dei Lavoratori 54
> 20092 Cinisello Balsamo
> Milan
> E-mail: a.stevenazzi at italfarmaco.com
> Tel: +39-02-64433097
> -----Messaggio originale-----
> Da: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Per conto di David Mobley
> Inviato: giovedì 16 marzo 2006 0.59
> A: Discussion list for GROMACS users
> Oggetto: Re: R: [gmx-users] Dihedral restraints
>
> Regarding dihedral restraints in 3.2, the dihres.c section of code
> only was a placeholder in 3.2 (it printed out "dihedral restraints on"
> but the dihedral restraints did nothing) but was fixed (sort of)
> before release of 3.3. I think the forces were still wrong in t he 3.3
> release, though, so even if you get 3.3 working, you will probably
> need to get the fixed dihres.c.
>
> I do, however, probably have a dihres.c floating around somewhere that
> would work properly with 3.3, and possibly also with 3.2 (at one point
> David van der Spoel wrote the section of code after I discovered it
> was missing from the 3.2 release). If you are desperate I can dig
> around for it.
>
> Thanks,
> David
>
>
> On 3/15/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>   
>> STEVENAZZI ANDREA wrote:
>>     
>>> Dear David
>>> I did check the mailing list archives and could not find anything
>>> related to.
>>> Moreover, I have experienced some problems with version 3.3 of Gromacs
>>> related to PME (see the mailing list archives) and I was forced to
>>> install the 3.2.1 version in order to run a simulation.
>>>       
>> There is a workaround for this too on the ftp site.
>>
>>     
>>> So you are telling me that dihedral restraints can not be set up in the
>>> 3.2 version?
>>>       
>> Don't recall but probably not.
>>
>>     
>>> I beg you pardon if these are stupid questions, but I have started to
>>> use Gromacs just 2 weeks ago.
>>> Thanks
>>> Andrea
>>>
>>>
>>>
>>> STEVENAZZI ANDREA wrote:
>>>       
>>>> Dear Gromacs Users
>>>>
>>>> I am trying to use Gromacs for the MD of a small modified peptide
>>>>         
>>> (just
>>>       
>>>> 4 residues with one ethylated) and I would like to set up one dihedral
>>>>         
>>>> restraint in the topology file.
>>>>
>>>> I have not found anything useful on the paper manual regarding
>>>>         
>>> dihedral
>>>       
>>>> restraints and thought that it might not be possible to set them.
>>>>
>>>> However, analysing the mdout.mdp file I realised that the keyword
>>>>         
>>> dihre
>>>       
>>>> (dihedral angle restraints) is actually there and can be turned on.
>>>>
>>>> If that is true, does anybody know the right lines to insert in the
>>>> topology file in order to set properly a dihedral restraints?
>>>>
>>>> Thanks
>>>>         
>>> manual is a bit outdated. check mailing list archives. it is possible
>>> with 3.3
>>>       
>>>> Best regards
>>>>
>>>> Andrea
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Andrea Stevenazzi
>>>>
>>>> Medicinal & Computer Chemistry
>>>>
>>>> Italfarmaco Research Centre
>>>>
>>>> Italfarmaco SpA
>>>>
>>>> Via dei Lavoratori 54
>>>>
>>>> 20092 Cinisello Balsamo
>>>>
>>>> Milan
>>>>
>>>> E-mail: a.stevenazzi at italfarmaco.com
>>>>         
>>> <mailto:a.stevenazzi at italfarmaco.com>
>>>       
>>>> Tel: +39-02-64433097
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>         
>>> ------------------------------------------------------------------------
>>>       
>>>> _______________________________________________
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>>>>         
>>>       
>> --
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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>>     
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