[gmx-users] energy minimization of POPC crash

Shan shan Qin sansanqin00 at mails.tsinghua.edu.cn
Mon May 14 07:30:31 CEST 2007

Hello,everyone.I want to simulate a membrane protein using 
inflategro to construct the initial structure,( http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis )
and I did the job like this:

First I got the equalibrated structure of POPC bilayer from Tileman's website,put 1RHZ
right at the centre of lipid bilayer.Then the coordinates of protein were rstricted, and the
coorinates of lipids were rescaled by a factor 4, next I cut off all the lipids within a distance of 14 A from protein ,rescaled lipids coordinates by 0.95,and cut off lipids within 14A from protein.Then I restriction the position of protein and minize the energy of lipids.However the minimization always crash.

So will somebody please tell me how to construct the initial simulation structure  of membrane protein using "dig hole" method in detail? and why the em crash? I have tried all the methods I could find but they just didn't work.You are very thankful to offer some help.
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