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

From: Ross Walker <>
Date: Wed, 13 May 2015 11:03:23 -0700

Hi Him,

You are running a simulation here with anisotropic pressure scaling so it is perfectly reasonable that the shape of your simulation box can change during the simulation. The structure from Charmm-gui is most definitely not equilibrated and lipid membranes are somewhat fluid structures so it is not unreasonable to expect the ratio of the box lengths to change.

Note your volume - 68^3 = 314,432 A^3 vs 76x59x69 = 309,396 A^3 represents only a 1.7% change so your density has not changed very much despite the relative box lengths changing.

All the best

> On May 13, 2015, at 10:26 AM, Him Shweta <> wrote:
> 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 - 11:30:03 PDT
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