[gmx-users] Simulation of membrane associated protein

[Olga Press]

Dear all,
I am working on DOPC-associated protein and try to orient the protein on
the DOPC surface by using the gmx_solvate as previously suggested by Prof.
Justin Lemkul at the following like
http://www.mdtutorials.com/gmx/biphasic/03_tricks.html
<https://www.researchgate.net/deref/http%3A%2F%2Fwww.mdtutorials.com%2Fgmx%2Fbiphasic%2F03_tricks.html>
.
The protein reaches the desired position, however together with the TIP3
molecules, there is a removal of several lipids, although there was no
overlap between the protein and the lipids. (instead of 260 lipids I get
243 lipids)
What can I do to prevent removal of lipids? any suggestions?
I checked it with the default vdw distance (0.105) and also with modified
vdwradii.dat were the C radius was set to 0.15.
Moreover, the gmx_solvate removes an odd number of lipids, meaning one
layer has fewer lipids.
I would much appreciate any help.
Thank you!


-- 
*Olga Press-Sandler*
Ph.D. student, Yifat Miller's lab
Department of Chemistry
Ben-Gurion University, Israel