[gmx-users] water.pdb file

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 11 00:31:32 CEST 2009

sunny mishra wrote:
> Hi Justin,
> Thanks for the expedient reply. In the MARTINI tutorial they have
> provided two water.gro files one for lipids and the other for
> proteins. Protein water molecule file consists of 10800 atoms of water
> and the lipid has 400 atoms. So even if I simulate any protein
> structure after converting that to CG, can I use the same water.gro
> file for protein always?

I don't know about different water files based on the system; that seems a bit 
arbitrary.  I'm referring to the one single water.gro file here:


If there are differences between using the water structure with proteins and 
lipids, any changes are likely reflected in the force field, version 2.0 for 
lipids, and version 2.1, which is the extension to proteins, if there is a 
difference at all.  Any reasonable equilibrated box of water will probably 
suffice; your equilibration will likely take care of any differences, if they exist.


> 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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