[gmx-users] water.pdb file

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 11 00:01:26 CEST 2009

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.


> 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


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