[gmx-users] Membrane simulations

[Justin Lemkul]

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.
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
> 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:

#include "lipid.itp"
#include "dopc.itp"
#include "spc.itp"

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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