[gmx-users] RE: How to use Inflategro with different lipid types

Ioannis Beis ibeis at mail.student.oulu.fi
Mon May 2 10:14:39 CEST 2011


I would like to thank Justin and Tom for their kind replies to my  
question! I believe that by having the gromacs manual as a guide I  
would manage to bring the bilayer into physiological size by using  
Justin's advice. However, Tom's advice sounds simpler to implement.  
Unfortunately the size of the pre-equilibrated POPC is too small for  
what I want to do afterwards, but I can make my own POPC using  
editconf, genconf and Inflategro to shrink and equilibrate it first  
and then use the renaming trick.

For beginner users that will consult this thread in the future, I had  
overestimated the value of the coordinate files as starting  
structures... Deleting the last two united atoms from oleoyl will fix  
the hydrocarbon chain length and using a palmitoyl force field will  
take care of turning the double bond into a single one. Renaming the  
three different united atoms' names in the polar heads and eventually  
the names of the whole lipids is like turning ethanolamine into  
choline and vice versa. The initial positions at the crucial points  
will be very improper, but this isn't important since hopefully the  
energy minimization will fix them. This strategy -with a little more  
work- could even be applied for more diverse polar heads as soon as  
one has a force field, just by placing his atoms at very reasonable  
initial positions! Proper topology file is all that matters :).

Thanks again for your ideas!


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