[gmx-users] EM in kalp15_DPPC

Justin Lemkul jalemkul at vt.edu
Tue Aug 21 12:39:24 CEST 2012

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



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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