[AMBER] DOPC lipid bilayer in Amber using lipid14 force field.

From: Him Shweta <shwetahim.gmail.com>
Date: Wed, 13 May 2015 22:56:26 +0530

Hi all,

I am running DOPC lipid bilayer simulation in AMBER12 using Lipid14 force
field following lipid14 tutorial in K20 GPU after equilibarting in CPU for
4 ns. Initial structure is made through Charmm-GUI online site. The initial
box size for the simulation is 68 x 68 x 68 angstrom. System has 64 lipid
in each bilayer using 32 water molecules per lipid.
After running a simulation of 65 ns, shrinkage in the box size is seen. Box
size is now 76 x 59 x 69 angstrom. I could not understand why the box is
shrinking. Is there any issue in the force field or is because of running
the simulation in GPU. Area per lipid calculated is 69.4 angstrom squared.

Any suggestions would be appreciated. Thanks.
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Received on Wed May 13 2015 - 10:30:08 PDT
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