[gmx-users] EM in kalp15_DPPC

[Justin Lemkul]

On 8/21/12 6:35 AM, Shima Arasteh wrote:
> Allright, I will check the configurations of out and inputs to find out the reason of warning.
> Please let me know something:
> Should I expect to see changes in area per lipids in each shrinking or it would happen after 25th repeat suddenly?
>

It will decrease steadily.  Make sure your loop is calling the correct 
coordinate file each time.  The energy-minimized output of the previous step is 
the input into the next iterations of shrinking, i.e.:

system_inflated.gro -> em_inflated.gro
em_inflated.gro -> system_shrink1.gro -> em_shrink1.gro
em_shrink1.gro -> system_shrink2.gro -> em_shrink2.gro
etc.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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