[gmx-users] Rigid molecules in system

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 8 09:18:10 CET 2005

On Tue, 2005-03-08 at 08:21 +0800, xzp02 at mails.tsinghua.edu.cn wrote:
> Dear all:
>     I want to study a system with 2 molecules(C1 and C2), and I do not need the
> intramolecular degree of freedom (loss of reality) but care of the intermolecular
> vdW interaction. Can anyone help me with the method?
>     And also I wonder if the total energy is conserving in that case ?
You have to be more specific. You can specify constraints until there is
no possible intramolecular motion, but there is no easier way of
specifying the molecules are rigid. With constraints you can still have
reasonable energy conservation, but not perfect since it involves an
optimization algorithm with a tolerance.

> Best,
> ZP 
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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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