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
--
========================================
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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