[gmx-users] grompp -r option

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 18 17:14:36 CEST 2002

On Wed, 2002-09-18 at 15:38, hugo verli wrote:
> Hi to all,
> I have some doubts about a previously discussed subject here in mail list. 
> When I use the option -r in grompp, adding extra coordinates for the
> restraining positions, from where the program retrieves the restraint forces?
> >From a .itp file? So in the .mdp should I put a define =  -DPOSRE option?
It is defined in the topology which atoms are restrained. You need to
check the .top file. By default a conditional include is generated by
pdb2gmx to turn on position restraints. Chapter 5 in the manual explains

> Many thanks in advance,
> Hugo Verli.
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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