AMBER Archive (2002)

Subject: Re: Problems during equilibration

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You are right. I was missing the "imaging" step of the trajectory
post-processing before visualization.

Thanks to everybody who replied.

--- Holger Gohlke <gohlke_at_scripps.edu> wrote:
> Hi,

> Your pictures look pretty normal to me. You probably did not image
> your
> snapshots before extracting them from the trajectory? During your
> simulation, the water molecules diffused to the surrounding boxes of
> your periodic boundary setup.

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• Next message: Yongjun Jiang: "why are the results so large difference calculating by mm_pbsaandmm_gbsa?"
• Previous message: Carlos Simmerling: "Re: Strange MD simulation results with GB solvation at high temp."
• Maybe in reply to: Pratul Agarwal: "Problems during equilibration"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]