[gmx-users] constarint algorithm
David van der Spoel
spoel at xray.bmc.uu.se
Fri May 10 14:40:42 CEST 2002
On Fri, 10 May 2002, Dmitry Kovalsky wrote:
>I wonder about the possible distortion of a calculated protein trajectory, if
>LINCS or SHAKE is used. In other words, what is the best correlation of
>timestep-constraint_algortithm vs. protein_structure_rigidity?
I'm not sure I understand the question.
The use (or not) of constraints determines the maximum timestep. Together
they determine the accuracy of the integration algorithm.
If we assume that the timestep is sufficiently short, such that the
accuracy of integration does not influence the results, then the protein
rigidity is determined by other parameters, most notably:
- cut-off treatment (short cut-offs give large errors)
- force field
- system size
- presence of salt
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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