[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
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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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