wuxiao wrote:
Dear gmx users,
On current, I plan to study a dendrimer (like PAMAM) using MD
simulations available in GROMACS. As is well-known, the .gro and .top
files are the start points for running MD simulations in GROMACS.
However, the question how to obtain the files for dendrimers puzzles me
too much, since the dendrimers have a complex dendritic structure. The
mail-list and the manual seem not give helpful clues on doing it. Are
there someone that have the experiences to do so? Could you share these
experiences with us? Any suggesstion would be acknowledged greatly.
Chaofu Wu, Dr.
You will need to write your own rtp entries. Terminating chains may be a
problem, but I don't know the structure and composition of these
molecules, so it is hard to judge.
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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
[email protected] [email protected] http://folding.bmc.uu.se
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