RE: margin value

From: M. Madhu (madhu7_at_hotmail.com)
Date: Tue Jun 12 2007 - 17:19:26 CDT

Hi Peter,

Thank you very much for your reply. You cleared all my doubts.

Madhu

----------------------------------------
> Date: Tue, 12 Jun 2007 15:28:48 -0500
> From: petefred_at_ks.uiuc.edu
> To: madhu7_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: margin value
>
> Hi Madhu,
> the margin shouldn't have any physical effect on the simulation -- all
> that it does is change how namd splits up the system into patches for
> the simulation. However, if you're doing an NPT simulation, you should
> not expect to get identical results between runs -- please see the
> discussion of the seed keyword at
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node26.html.
> The margin keyword itself is discussed at
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node26.html#5124
> Peter
>
> M. Madhu wrote:
> > Hi NAMD users,
> >
> > During my TMD simulation (NPT) in a lipid bilayer, I get the following fatal error.
> > ================================
> > FATAL ERROR: Bad global exclusion count!
> >
> > FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: Bad global exclusion count!
> >
> > FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
> > ================================
> >
> > However, It works without any warning If use a margin value greater than 50.
> > I tried with margin 50 and margin100. According to NAMD user's guide margin
> > parameter will not change the physical results of the simulation. But the final
> > energies obtained with margin 50 and 100 are different.
> >
> > Cany anyone tell me what exactly this parameter is doing in the simulation?
> > How this parameter retains the physical results with different margin values,
> > though the final energies are different?
> > Whether a large margin value (eg: 50) causes any adverse effects in the simulation.
> >
> > Thanks,
> > Madhu
> >
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