[gmx-users] Best strategy to set up a system for an Umbrella sampling simulations

[Carlos Navarro Retamal]

Dear gromacs users,
I want to analyse the interaction between a protein an several biological membranes (including POPC membrane and some glycopilids). In order to do this i want to follow the protocol found here -> http://www.sciencedirect.com/science/article/pii/S0005273612002581
Where at an specific distance they pulled the protein to the membrane in order to insert it peripherally (through the charged groups) ,in order to sample the specific reaction coordinate for the PMF calculation.
I read several protocols to embed a protein into a membrane, and since that i’m not familiar working with lipids molecules, i have no idea how i can place the protein peripherally (i.e orient at a 90º: this protein posses a hairpin-like alpha helical conformation) at an specific distance.
I know that insany.py can be used for this task in a CG simulation, but since i’m planning to perform a AA simulations, i don’t think that i can use this tool.
Probably is a silly question, but i hope someone can help me.
Best regards,
Carlos

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Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl