[gmx-users] lipid-protein simulation
shima_arasteh2001 at yahoo.com
Sun Sep 16 18:34:22 CEST 2012
To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering:
1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water?
2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions.
Would you please help me?
Thanks in advance.
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