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
--
========================================
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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