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

[Justin Lemkul]

On 3/6/15 11:08 PM, Carlos Navarro Retamal wrote:
> 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.

editconf has options to rotate and translate.  Use those to place the peptide 
appropriately within the box.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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