[gmx-users] How to obtain the .gro and .top files for dendrimers

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 18 11:06:51 CEST 2009

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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