On May 7, 2014, at 8:00 AM, Vijay Manickam Achari <vjrajamany.yahoo.com> wrote:
> Dear sir,
>
> I have tried to re-image my bilayer (with water and lipids) after the simulation about 300 ns.
> I use the command "autoimage" as prescribed in AmberTools and my earlier posts.
>
> But my trials went no avail.
>
> I used commands like below, one after one in my trials in cpptraj:
>
> 1) autoimage
>
> 2) autoimage origin
>
> I also used ptraj:
ptraj and cpptraj use the same imaging routines (except cpptraj has "autoimage"). Any imaging command you can run in ptraj will do the same thing in cpptraj. I point this out only because ptraj is not installed by default starting with AmberTools 14.
> center *
> image center
>
> But all didnt work for me. I can see the bilayer shifts slowly in the box and the water molecules in one layer shift to another layer.
Maybe try the "anchor" keyword in autoimage, and anchor a specific lipid molecule in the autoimage command. Or alternatively you could anchor the tail of one of the lipid residues.
The lipid tutorial (
http://ambermd.org/tutorials/) also has a sample cpptraj/ptraj script that performs imaging.
Most importantly, keep trying stuff until you are satisfied with the imaging (but also make sure you can recognize something that is an imaging artifact vs. an actual effect).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 07 2014 - 06:00:09 PDT
