[gmx-users] Membrane simulations
jalemkul at vt.edu
Sun Apr 21 17:07:09 CEST 2013
On 4/21/13 10:40 AM, Sun Moon wrote:
> Dear all,
> I want to simulate DOPC membrane.I used the following site to find force field and topology files.
> I have two questions:
> 1.This site design to simulate protein membrane not membrane. Should i use dopc.itp with lipid.itp to simulate DOPC ?
Your assertion is incorrect. The lipid parameters were originally used for pure
membrane simulations (read Tieleman's papers). The fact that they are
compatible with some protein force fields is a separate point.
> 2.How to apply ffg53a1 for simulating dopc? If your answer about before question is yes. The following topology.itp is correct to continue?
> # include “ ffG53a6_lipid.itp”
> # include “ dopc.itp”
> # include “ spc.itp”
In theory, for pure lipid simulations, one does not even need a Gromos96
parameter set at all. For a pure membrane:
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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