sunny mishra wrote:
Hi all,
Thanks for all the previous help. I am starting to run my protein
simulations after going through the MARTINI tutorial. In MARTINI
tutorials I was provided with some of the input files but they have
also taught that how to make your own input files when you run your
own protein simulation. I have a quick question that I know how to
make all GROMACS input files except the water molecule files. I don't
know how to create water.pdb file on my own.
There is a suitable water structure on the MARTINI site. Since each particle
represents four(?) water molecules, I don't think it would be trivial to create
such a file on your own from an existing atomistic structure (or from scratch).
Probably best to use theirs.
-Justin
Suggestions will be highly appreciable.
Thanks,
Sunny
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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