(no subject)

From: David Rogers (wantye_at_gmail.com)
Date: Mon Apr 11 2011 - 22:26:09 CDT

Hi Buddhadev,

  I've seen separation of the two membrane leaflets using charmm
protein-lipid forcefields after very long dynamics runs with KcsA and
ClC-ec1, independent of NPT or Nz(gamma)T (with isotropic P=1).
Without more information on your system or equilibration protocol,
there's not much I can say except to vary the pressure / surface
tension / try constant volume, quantify your lipid density against
published protocols, etc. If the system is really periodic, there's
no special reason the corners would have gaps over the rest of the
system. Gromacs has a nice tool for building periodic copies of your
system to check for gaps in the corners though.

~ David Rogers

On Mon, Apr 11, 2011 at 3:27 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu> wrote:
> Dear NAMD Users,
> I am working on membrane simulation. I did long NPT run to compress the box and no undesirable gaps present between the periodic images of box. After that I switch to NPT ConstantArea production run. I am getting immediately gaps between the periodic images basically in corner. And also the gaps are in between protein and lipids. If I go for more production run, the gaps are growing more and I am getting unphysical results. Could you please reply me any suggestions, it will be great help for me.
> Have a nice day,
> Thanks,
> Maiti

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