David van der Spoel
spoel at xray.bmc.uu.se
Tue May 17 13:41:12 CEST 2005
On Tue, 2005-05-17 at 12:30 +0100, Joanne Hanna wrote:
> Many thanks for this reply.
> Would you be able to tell me what the value range is for the position restraints, is 1000 the max? and what do these values mean in terms of the strength or flexibility in the restraint. I have had a look in the manual but could not locate the section relating to the inference of these values.
You can go higher but will get faster fluctuations, in the end forcing
you to reduce your time step.
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> CV4 7AL
> J.F.Hanna at warwick.ac.uk
> jfhanna at gmail.com
> >>> feenstra at few.vu.nl 05/11/05 12:21 PM >>>
> David van der Spoel wrote:
> > On Fri, 6 May 2005, Joanne Hanna wrote:
> >>Thank you, I had misunderstood what the purpose of the position restraints file. If I have a protein posre.itp and ligand posre.ipt files do i leave them all as seperate files of the same name or do I combine then, also where do i define the force constant and if i have had to make a topology file (which I have had to for an AMP ligand) how do i generate a position restraints file for this?
> > there is a utility called genpr
> Position restrains, in Gromacs, are a property of a certain molecule
> type, e.g. your protein or the AMP. Each of molecules that you want to
> restrain, will need its own [position_restraints] section. This you
> could add (manually) to the molecule's .top or .itp file, but more
> commonly it is included into the respective file by an '#include'
> statement, like:
> -- file protein.top --
> protein ...
> #ifdef POSRE
> #include posre.itp
> #include AMP.itp
> --- end of file protein.top --
> And the AMP.itp would look like:
> AMP ...
> #ifdef POSRE
> #include posre_AMP.itp
> The posre*.itp file would look like
> 1 1 200
> 2 1 200
> 3 1 200
> Where 1, 2, 3 are the atom numbers to be restrained, i.e. one for each
> atom in your molecule. This may be hundreds or thousands for your
> protein, and several tens for your AMP. Indeed, for this part there is a
> tool called 'genpr' which acccepts an index file and will write a posre
> file for one index group (set of atoms).
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://xray.bmc.uu.se/~spoel
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