[gmx-users] distance restraints and periodic image
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 2 10:52:22 CEST 2002
On Mon, 2002-09-02 at 10:08, jozef hritz wrote:
> Dear gmx-people,
> I use distance restraint inside "one molecule" which consists of two parts
> A, B. Normal distance restraint lenght is 0.5 nm. During MD everything is
> OK until part A jump to its periodic image and distance restraint is
> applied between B in original box and A in next periodic cell. Now
> distance lenght is 3 nm and very strong (artificial) force between A B is
> applied. B in original box is moving to A in next box.
> How to apply normal distance restraint between A, B in original box?
> I also don't understand why A jump to its periodic image, when only small
> part of it is out of box. Is there opportunity let A in original box
> during whole MD? (I am not talking about visualisation)
It sounds like a bug. If I understand you correctly your two parts of
the molecule (A and B) are only connected by distance restraints?
Which gmx version are you running. It seems that this is fixed in the
CVS version already.
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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