Re: problem when do equilibration

From: JC Gumbart (
Date: Sun Aug 21 2005 - 14:14:12 CDT

It is possible that when you first equilibrate, if you are running
constant pressure, that the cell shrinks noticeably early in the
simulation. When this happens, the patch grid that was originally
assigned is insufficient and atoms fall outside of the boundaries. A
margin gives some extra space for atoms to move beyond the patch.

None of this is physical though, just related to the way NAMD
internally divides the space. I think too big a margin will slow
things down so I wouldn't use it unless necessary (as it is here).

See Kale, et al., Journal of Computational Physics 151: 283-312.

On Aug 21, 2005, at 11:09 AM, Pedro Borkowski wrote:

> Someone suggested to me that the margin should be set to 2.5.
> I tried this and I never had this problems with any of my
> simulationsafter that.
> You can try that, but if anyone in the NAMD community can explain
> why2.5 is such a special number I would really like to know.
> Thanks
> -Pedro Borkowski
> On 8/21/05, 吴洪明 <> wrote:> > > > Hi, > > I run
> namd for equilibration and after about 10000setps,occur the problem >
> > > > FATAL ERROR: Periodic cell has become too small for original
> patch grid! > > Possible solutions are to restart from a recent
> checkpoint, > > increase margin, or disable useFlexibleCell for liquid
> simulation. > > > > > > How can I solove this ???
> -- -Pedro Borkowski

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