[gmx-users] Can the structure built by Amorphous Cell of Materials Studio be used for GROMACS inputs?

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 25 12:43:02 CEST 2007

wuxiao wrote:
> Hi, everybody,
> I am a freshman for using GROMACS. I used to do simulations using 
> Materials Studio. Now I notice that versatile analysis tools are present 
> in GROMACS, so I decide to turn for GROMACS. I have built some polymeric 
> structures using the Amorphous Cell module in Materials Studio4.0. Can 
> these structures be directly input into GROMACS for a further 
> simulations? How can I do that? Can you give some hints?
> Thanks a lot in advance.
you can do polymer simulation in gromacs, but you need to built the 
topology file by hand, or using some kind of script that you write. if 
you have few different monomers you could build residues for use in 
pdb2gmx as well.
chapter 5 in the manual.

> Xiaowu
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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://folding.bmc.uu.se

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