[gmx-users] how to describe spring between core and shell

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 6 10:47:52 CET 2005

sangyongliang99 at mails.tsinghua.edu.cn wrote:

>Dear Erik and David:
>I am very much thankfull for your kind help before!
>But I have another question which is about how to describe spring const of core
>and shell in shell model.My model is  a shell connecting to a core, not to a dummy
>particle as in sw.itp, so should I describe the spring using
>I also have some questions about the position_restraints in sw.itp as follows:
>[ position_restraints ]
>; See notes above.
>; i	funct	kx	ky	kz	rOH	rHH	rOD
>1	2 	608069	563101	586116	0.09572	0.15139 0.0137408
>1	2 	585318 	585318 	585318 	0.09572 0.15139 0.0137408
>Where is the atom 1 restrained? What does funct 2 mean?

This looks like a very old itp file, and probably a very old gromacs 
too... Pluease update to a more recent version and use the included 
sw.itp file.

>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

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

More information about the gromacs.org_gmx-users mailing list