[gmx-users] POPC Membrane + protein dynamics

padhu at ncbs.res.in padhu at ncbs.res.in
Fri Feb 26 07:44:26 CET 2010

Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
simulation of my protein within the POPC membrane. I have downloaded the
128a popc lipid from Prof.Tieleman's group along with the required
popc.itp. My protein of interest is 458 residues. Since the 128a popc is
already Simulated for 1600 ps, i haven't done membrane only simulation. So
i directly aligned my protein with the membrane using VMD and have saved
the coordinates. However after i aligned my protein with the membrane, i
felt the membrane was not big enough for my protein of interest, also, the
N-terminal region and the loop regions in the C-terminal region and
stretching outside water molecule above and below respectively.ow, i have
two questions here...
1. How would i increase the number of lipids from the existing one?
2. Also, i should increase increase the number of water molecules above
and below the membrane so that it covers the whole region of N-terminal
and also the loop regions of the C-terminal.
Now, How to perform these tasks??If i do so will it be compatible with the
popc.itp file which i downloaded from the Prof. Tieleman's group?

3. My third question is while aligning my protein with the membrane should
i make a hole first or after aligning the protein should i remove the
overlapping lipids with the proteins?which one would be better??

I have tried out some of the methodologies available in the internet but
it dosen't help me.If anyone of you have a detailed step by step
methodology right from the first step to till running the MD simulation
please let me know.
Your help will be highly appreciated.
Looking forward to hear from you.

Best regards

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