[gmx-users] compressing waterbox

[Justin A. Lemkul]

madhumita das wrote:
> Hi,
> 
>            I have genrated a membrane protein system solvated in a water 
> box.But the water molecules are found as loosly packed. Is there any 
> program or method to shrink a system in a water box like inflategro for 
> lipids?

The better solution is to solvate only once you have achieved the desired 
dimensions for the membrane after packing the lipids.  If you solvate too early, 
your system will be unstable or will take a long time to equilibrate, at least.

Some might suggest applying higher pressure to compress the system, but I think 
that will alter the lipid dynamics too much.  The best solution is better 
construction.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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