R: [gmx-users] Dihedral restraints

[David van der Spoel]

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 manual is a bit outdated.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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