May someone further interrogate these suggestions using center / unwrap
commands in the same cpptraj script ? BTW I also had positive experiences
using gromacs with membrane while it was also very complex routine
consisted many intermediate steps
.Stéphane - would it be possible to share a short video of your md system
in order that we may understand how the lipids behave on the border of the
box ??
All the best
Enrico
Il giorno ven 8 nov 2024 alle ore 10:00 Téletchéa Stéphane via AMBER <
amber.ambermd.org> ha scritto:
> Le 07/11/2024 à 16:25, Enrico Martinez via AMBER a écrit :
> > P.S. just testing the autoimage moveanchor I noticed that it produced a
> > very chaotic lipid distribution outside the simulation box, which
> contained
> > only protein and solvent .. ;-D
> Hi all,
>
> According to my tests, autoimage do not easily consider lipid like
> proteins, or,
> probably, lipids move too fast to ensure that the system stays whole.
>
> On one of my systems, I did also found that the protein was moving close
> to an edge of the box,
> so i understand why the algorithm fails in finding a goog "central point".
>
> Results of my experiments are:
> a) for newer systems use a bigger membrane setup with roughly z
> direction being half of the xy dimensions,
> for instance --dist_wat 50 --distxy_fix 100 in packmol-membgen
> b) use "iwrap=1" for the md trajectory
>
> c) for already produced trajectory, my best findings were to:
> (a) first use the "unwrap" command to reposition everything in one
> box :
>
> unwrap ":1-218" # where :1-218 is the protein, to ensure at least the
> protein is in the same box
> center ":1-218" mass origin # Center the system on the protein
> image origin center familiar # Center everything on the protein
> center ':PA,PC,OL' # Then center on the membrane to see evolution of the
> system over time
>
> This could not be applied blindly for all systems but allowed me to
> produce nice trajectories
> of my membrane systems suitable for publication
> (https://www.biorxiv.org/content/10.1101/2024.10.02.616265v1)
>
> HTH,
>
> Stéphane
>
> PS : this problem is complex, I also encounter this problem using GROMACS,
> I'm not sure there is a final algorithm able to handle all cases
> properly...
> There are literature concerns about it, though, see for instance:
>
> Bart M. H. Bruininks, Tsjerk A. Wassenaar, and Ilpo Vattulainen
> Journal of Chemical Information and Modeling 2023 63 (11), 3448-3452
> DOI: 10.1021/acs.jcim.2c01574
>
> --
> Maître de conférences Hors Classe, PEDR, HDR
> US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics,
> F-44000 Nantes
> http://www.us2b.univ-nantes.fr/ -http://www.steletch.org
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Received on Fri Nov 08 2024 - 01:30:01 PST
