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.
________________________________________________________________________
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
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